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#include "ButtonLed.h"

// These are ButtonLeds our newly created data type
// they hold both an led's pin and the pin for the button
// that turns it on
ButtonLed button1 = {1, 10};
ButtonLed button2 = {2,  8};
ButtonLed button3 = {9,  7};
ButtonLed button4 = {11, 6};
ButtonLed button5 = {12, 5};
ButtonLed button6 = {13, 4};

// This function will randomly shuffle an array of ButtonLeds
void shuffleArray (ButtonLed arr [], const int size){
    for (int i = 0; i < size - 1; i++){ // iterates through array except last element
        int j = random(0, size); // generates a random index from (0 to n-1) inclusive
                    
        // swap current index with random index
        ButtonLed t = arr[i]; 
        arr[i] = arr[j];
        arr[j] = t;
    }
}

ButtonLed getButtonPress (ButtonLed arr [], const int size){
    bool pressed = false;
    ButtonLed  pressedButton;
    while (!pressed){ // loops until a button was pressed
        for (int i = 0; i < size && !pressed; i++){ // !pressed allows early out
            if (digitalRead(arr[i].buttonPin)){ // one of the six buttons was pressed
                digitalWrite(digitalRead(arr[i].ledPin, HIGH); // turns on the led the user chose
                delay(200);
                digitalWrite(digitalRead(arr[i].ledPin, LOW); // turns it back off
                pressed = true; // exit both loops
                pressedButton = arr[i]; // stores which button was pressed
            }
        }
    }
    return pressedButton; // return the pressed button
}



void setup() {
    randomSeed(analogRead(A0));
    // This is how you set up the leds for output
    pinMode(button1.ledPin, OUTPUT);
    pinMode(button2.ledPin, OUTPUT);
    pinMode(button3.ledPin, OUTPUT);
    pinMode(button4.ledPin, OUTPUT);
    pinMode(button5.ledPin, OUTPUT);
    pinMode(button6.ledPin, OUTPUT);

    // This is how you set up the buttons for input
    pinMode(button1.buttonPin, INPUT);
    pinMode(button2.buttonPin, INPUT);
    pinMode(button3.buttonPin, INPUT);
    pinMode(button4.buttonPin, INPUT);
    pinMode(button5.buttonPin, INPUT);
    pinMode(button6.buttonPin, INPUT);
}

void loop() {

    // This array is of type ButtonLed our newly created data type
    ButtonLed questionNumberArray[] = {button1, button2, button3, 
                                       button4, button5, button6}; 
    const size_t n = 6; // array's size

    shuffleArray(questionNumberArray, n);

    
    
    bool guessCorrectly = false;

    // this while loop allows the user to keep trying until they get it right
    while (!guessCorrectly){


        // This loop displays the correct sequence to the user
        for (int i = 0; i < n; i++){
            digitalWrite(questionNumberArray[i].ledPin, HIGH); // turn on the led

            delay(500); // decrease this number to flash faster; increase to flash slower

            digitalWrite(questionNumberArray[i].ledPin, LOW); // turn off the led
        }
    
    
        bool correctButton = true; // the user has pressed the correct button
        ButtonLed userSequence [6];      // stores the sequence the user entered
        // lets the user push 6 buttons
        for (int i = 0; i < n; i++){
            userSequence[i] = getButtonPress(questionNumberArray, n);
            delay(500); // delay between button presses
        }

        // check if the user entered the correct sequence
        for (int i = 0; i < n && correctButton; i++){ 
            if (userSequence[i].buttonPin != questionNumberArray[i].buttonPin)
                correctButton = false;
        }

        if (correctButton){ // user entered the correct sequence
            guessCorrectly = true;
            // This will turn on the leds in the correct sequence
            for (int i = 0; i < n; i++){
                digitalWrite(questionNumberArray[i].ledPin, HIGH); // turn on the led
                delay(500); // delay half a second
                digitalWrite(questionNumberArray[i].ledPin, LOW); // turn off the led
            }
        }
    }
}

#include "ButtonLed.h"

// These are ButtonLeds our newly created data type
// they hold both an led's pin and the pin for the button
// that turns it on
ButtonLed button1 = {1, 10};
ButtonLed button2 = {2,  8};
ButtonLed button3 = {9,  7};
ButtonLed button4 = {11, 6};
ButtonLed button5 = {12, 5};
ButtonLed button6 = {13, 4};

// This function will randomly shuffle an array of ButtonLeds
void shuffleArray (ButtonLed arr [], const int size){
    for (int i = 0; i < size - 1; i++){ // iterates through array except last element
        int j = random(0, size); // generates a random index from (0 to size-1) inclusive
                    
        // swap current index with random index
        ButtonLed t = arr[i]; 
        arr[i] = arr[j];
        arr[j] = t;
    }
}

ButtonLed getButtonPress (ButtonLed arr [], const int size){
    bool pressed = false;
    ButtonLed  pressedButton;
    while (!pressed){ // loops until a button was pressed
        for (int i = 0; i < size && !pressed; i++){ // !pressed allows early out
            if (digitalRead(arr[i].buttonPin)){ // one of the six buttons was pressed
                digitalWrite(digitalRead(arr[i].ledPin, HIGH); // turns on the led the user chose
                delay(200);
                digitalWrite(digitalRead(arr[i].ledPin, LOW); // turns it back off
                pressed = true; // exit both loops
                pressedButton = arr[i]; // stores which button was pressed
            }
        }
    }
    return pressedButton; // return the pressed button
}



void setup() {
    randomSeed(analogRead(A0));
    // This is how you set up the leds for output
    pinMode(button1.ledPin, OUTPUT);
    pinMode(button2.ledPin, OUTPUT);
    pinMode(button3.ledPin, OUTPUT);
    pinMode(button4.ledPin, OUTPUT);
    pinMode(button5.ledPin, OUTPUT);
    pinMode(button6.ledPin, OUTPUT);

    // This is how you set up the buttons for input
    pinMode(button1.buttonPin, INPUT);
    pinMode(button2.buttonPin, INPUT);
    pinMode(button3.buttonPin, INPUT);
    pinMode(button4.buttonPin, INPUT);
    pinMode(button5.buttonPin, INPUT);
    pinMode(button6.buttonPin, INPUT);
}

void loop() {

    // This array is of type ButtonLed our newly created data type
    ButtonLed questionNumberArray[] = {button1, button2, button3, 
                                       button4, button5, button6}; 
    const size_t n = 6; // array's size

    shuffleArray(questionNumberArray, n);

    
    numLeds = 1;
    bool guessCorrectly = false;

    // this while loop allows the user to keep trying until they get it right
    while (!guessCorrectly){


        // This loop displays the correct sequence to the user
        for (int i = 0; i < numLeds; i++){
            digitalWrite(questionNumberArray[i].ledPin, HIGH); // turn on the led

            delay(500); // decrease this number to flash faster; increase to flash slower

            digitalWrite(questionNumberArray[i].ledPin, LOW); // turn off the led
        }
    
    
        bool correctButton = true; // the user has pressed the correct button
        ButtonLed userSequence [6];      // stores the sequence the user entered
        // lets the user push 6 buttons
        for (int i = 0; i < numLeds; i++){
            userSequence[i] = getButtonPress(questionNumberArray, numLeds);
            delay(500); // delay between button presses
        }

        // check if the user entered the correct sequence
        for (int i = 0; i < numLeds && correctButton; i++){ 
            if (userSequence[i].buttonPin != questionNumberArray[i].buttonPin)
                correctButton = false;
        }

        if (correctButton){ // user entered the correct sequence
            guessCorrectly = true;
            // This will turn on the leds in the correct sequence
            for (int i = 0; i < numLeds; i++){
                digitalWrite(questionNumberArray[i].ledPin, HIGH); // turn on the led
                delay(500); // delay half a second
                digitalWrite(questionNumberArray[i].ledPin, LOW); // turn off the led
            }
            numLeds++;
            if (numLeds > 6)
                --numLeds;
        }
    }
}

#include "ButtonLed.h"

// These are ButtonLeds our newly created data type
// they hold both an led's pin and the pin for the button
// that turns it on
ButtonLed button1 = {1, 10};
ButtonLed button2 = {2,  8};
ButtonLed button3 = {9,  7};
ButtonLed button4 = {11, 6};
ButtonLed button5 = {12, 5};
ButtonLed button6 = {13, 4};

// This function will randomly shuffle an array of ButtonLeds
void shuffleArray (ButtonLed arr [], const int size){
    for (int i = 0; i < size - 1; i++){ // iterates through array except last element
        int j = random(0, size); // generates a random index from (0 to n-1) inclusive
                    
        // swap current index with random index
        ButtonLed t = arr[i]; 
        arr[i] = arr[j];
        arr[j] = t;
    }
}

ButtonLed getButtonPress (ButtonLed arr [], const int size){
    bool pressed = false;
    ButtonLed  pressedButton;
    while (!pressed){ // loops until a button was pressed
        for (int i = 0; i < size && !pressed; i++){ // !pressed allows early out
            if (digitalRead(arr[i].buttonPin)){ // one of the six buttons was pressed
                pressed = true; // exit both loops
                pressedButton = arr[i]; // stores which button was pressed
            }
        }
    }
    return pressedButton; // return the pressed button
}



void setup() {
    randomSeed(analogRead(A0));
    // This is how you set up the leds for output
    pinMode(button1.ledPin, OUTPUT);
    pinMode(button2.ledPin, OUTPUT);
    pinMode(button3.ledPin, OUTPUT);
    pinMode(button4.ledPin, OUTPUT);
    pinMode(button5.ledPin, OUTPUT);
    pinMode(button6.ledPin, OUTPUT);

    // This is how you set up the buttons for input
    pinMode(button1.buttonPin, INPUT);
    pinMode(button2.buttonPin, INPUT);
    pinMode(button3.buttonPin, INPUT);
    pinMode(button4.buttonPin, INPUT);
    pinMode(button5.buttonPin, INPUT);
    pinMode(button6.buttonPin, INPUT);
}

void loop() {

    // This array is of type ButtonLed our newly created data type
    ButtonLed questionNumberArray[] = {button1, button2, button3, 
                                       button4, button5, button6}; 
    const size_t n = 6; // array's size

    shuffleArray(questionNumberArray, n);

    
    
    bool guessCorrectly = false;

    // this while loop allows the user to keep trying until they get it right
    while (!guessCorrectly){
        bool correctButton = true; // the user has pressed the correct button
        ButtonLed userSequence [6];      // stores the sequence the user entered
        // lets the user push 6 buttons
        for (int i = 0; i < n; i++){
            userSequence[i] = getButtonPress(questionNumberArray, n);
            delay(500); // delay between button presses
        }

        // check if the user entered the correct sequence
        for (int i = 0; i < n && correctButton; i++){ 
            if (userSequence[i].buttonPin != questionNumberArray[i].buttonPin)
                correctButton = false;
        }

        if (correctButton){ // user entered the correct sequence
            guessCorrectly = true;
            // This will turn on the leds in the correct sequence
            for (int i = 0; i < n; i++){
                digitalWrite(questionNumberArray[i].ledPin, HIGH); // turn on the led
                delay(500); // delay half a second
                digitalWrite(questionNumberArray[i].ledPin, LOW); // turn off the led
            }
        }
    }
}

#include "ButtonLed.h"

// These are ButtonLeds our newly created data type
// they hold both an led's pin and the pin for the button
// that turns it on
ButtonLed button1 = {1, 10};
ButtonLed button2 = {2,  8};
ButtonLed button3 = {9,  7};
ButtonLed button4 = {11, 6};
ButtonLed button5 = {12, 5};
ButtonLed button6 = {13, 4};

// This function will randomly shuffle an array of ButtonLeds
void shuffleArray (ButtonLed arr [], const int size){
    for (int i = 0; i < size - 1; i++){ // iterates through array except last element
        int j = random(0, size); // generates a random index from (0 to n-1) inclusive
                    
        // swap current index with random index
        ButtonLed t = arr[i]; 
        arr[i] = arr[j];
        arr[j] = t;
    }
}

ButtonLed getButtonPress (ButtonLed arr [], const int size){
    bool pressed = false;
    ButtonLed  pressedButton;
    while (!pressed){ // loops until a button was pressed
        for (int i = 0; i < size && !pressed; i++){ // !pressed allows early out
            if (digitalRead(arr[i].buttonPin)){ // one of the six buttons was pressed
                digitalWrite(digitalRead(arr[i].ledPin, HIGH); // turns on the led the user chose
                delay(200);
                digitalWrite(digitalRead(arr[i].ledPin, LOW); // turns it back off
                pressed = true; // exit both loops
                pressedButton = arr[i]; // stores which button was pressed
            }
        }
    }
    return pressedButton; // return the pressed button
}



void setup() {
    randomSeed(analogRead(A0));
    // This is how you set up the leds for output
    pinMode(button1.ledPin, OUTPUT);
    pinMode(button2.ledPin, OUTPUT);
    pinMode(button3.ledPin, OUTPUT);
    pinMode(button4.ledPin, OUTPUT);
    pinMode(button5.ledPin, OUTPUT);
    pinMode(button6.ledPin, OUTPUT);

    // This is how you set up the buttons for input
    pinMode(button1.buttonPin, INPUT);
    pinMode(button2.buttonPin, INPUT);
    pinMode(button3.buttonPin, INPUT);
    pinMode(button4.buttonPin, INPUT);
    pinMode(button5.buttonPin, INPUT);
    pinMode(button6.buttonPin, INPUT);
}

void loop() {

    // This array is of type ButtonLed our newly created data type
    ButtonLed questionNumberArray[] = {button1, button2, button3, 
                                       button4, button5, button6}; 
    const size_t n = 6; // array's size

    shuffleArray(questionNumberArray, n);

    
    
    bool guessCorrectly = false;

    // this while loop allows the user to keep trying until they get it right
    while (!guessCorrectly){


        // This loop displays the correct sequence to the user
        for (int i = 0; i < n; i++){
            digitalWrite(questionNumberArray[i].ledPin, HIGH); // turn on the led

            delay(500); // decrease this number to flash faster; increase to flash slower

            digitalWrite(questionNumberArray[i].ledPin, LOW); // turn off the led
        }
    
    
        bool correctButton = true; // the user has pressed the correct button
        ButtonLed userSequence [6];      // stores the sequence the user entered
        // lets the user push 6 buttons
        for (int i = 0; i < n; i++){
            userSequence[i] = getButtonPress(questionNumberArray, n);
            delay(500); // delay between button presses
        }

        // check if the user entered the correct sequence
        for (int i = 0; i < n && correctButton; i++){ 
            if (userSequence[i].buttonPin != questionNumberArray[i].buttonPin)
                correctButton = false;
        }

        if (correctButton){ // user entered the correct sequence
            guessCorrectly = true;
            // This will turn on the leds in the correct sequence
            for (int i = 0; i < n; i++){
                digitalWrite(questionNumberArray[i].ledPin, HIGH); // turn on the led
                delay(500); // delay half a second
                digitalWrite(questionNumberArray[i].ledPin, LOW); // turn off the led
            }
        }
    }
}

#include "ButtonLed.h"

// These are ButtonLeds our newly created data type
// they hold both an led's pin and the pin for the button
// that turns it on
ButtonLed button1 = {1,  0};
ButtonLed button2 = {2,  0};
ButtonLed button3 = {9,  0};
ButtonLed button4 = {11, 0};
ButtonLed button5 = {12, 0};
ButtonLed button6 = {13, 0};

// This function will randomly shuffle an array of ButtonLeds
void shuffleArray (ButtonLed arr [], const int size){
    for (int i = 0; i < size - 1; i++){ // iterates through array except last element
        int j = random(0, size); // generates a random index from (0 to n-1) inclusive
                    
        // swap current index with random index
        ButtonLed t = arr[i]; 
        arr[i] = arr[j];
        arr[j] = t;
    }
}

ButtonLed getButtonPress (ButtonLed arr [], const int size){
    bool pressed = false;
    ButtonLed  pressedButton;
    while (!pressed){ // loops until a button was pressed
        for (int i = 0; i < size && !pressed; i++){ // !pressed allows early out
            if (digitalRead(arr[i].buttonPin)){ // one of the six buttons was pressed
                pressed = true; // exit both loops
                pressedButton = arr[i]; // stores which button was pressed
            }
        }
    }
    return pressedButton; // return the pressed button
}



void setup() {
    randomSeed(analogRead(A0));
    // This is how you set up the leds for output
    pinMode(button1.ledPin, OUTPUT);
    pinMode(button2.ledPin, OUTPUT);
    pinMode(button3.ledPin, OUTPUT);
    pinMode(button4.ledPin, OUTPUT);
    pinMode(button5.ledPin, OUTPUT);
    pinMode(button6.ledPin, OUTPUT);

    // This is how you set up the buttons for input
    pinMode(button1.buttonPin, INPUT);
    pinMode(button2.buttonPin, INPUT);
    pinMode(button3.buttonPin, INPUT);
    pinMode(button4.buttonPin, INPUT);
    pinMode(button5.buttonPin, INPUT);
    pinMode(button6.buttonPin, INPUT);
}

void loop() {

    // This array is of type ButtonLed our newly created data type
    ButtonLed questionNumberArray[] = {button1, button2, button3, 
                                       button4, button5, button6}; 
    const size_t n = 6; // array's size

    shuffleArray(questionNumberArray, n);

    
    
    bool guessCorrectly = false;

    // this while loop allows the user to keep trying until they get it right
    while (!guessCorrectly){
        bool correctButton = true; // the user has pressed the correct button
        ButtonLed userSequence [6];      // stores the sequence the user entered
        // lets the user push 6 buttons
        for (int i = 0; i < n; i++){
            userSequence[i] = getButtonPress(questionNumberArray, n);
            delay(500); // delay between button presses
        }

        // check if the user entered the correct sequence
        for (int i = 0; i < n && correctButton; i++){ 
            if (userSequence[i].buttonPin != questionNumberArray[i].buttonPin)
                correctButton = false;
        }

        if (correctButton){ // user entered the correct sequence
            guessCorrectly = true;
            // This will turn on the leds in the correct sequence
            for (int i = 0; i < n; i++){
                digitalWrite(questionNumberArray[i].ledPin, HIGH); // turn on the led
                delay(500); // delay half a second
                digitalWrite(questionNumberArray[i].ledPin, LOW); // turn off the led
            }
        }
    }
}

Edit

#include "ButtonLed.h"

// These are ButtonLeds our newly created data type
// they hold both an led's pin and the pin for the button
// that turns it on
ButtonLed button1 = {1, 10};
ButtonLed button2 = {2,  8};
ButtonLed button3 = {9,  7};
ButtonLed button4 = {11, 6};
ButtonLed button5 = {12, 5};
ButtonLed button6 = {13, 4};

// This function will randomly shuffle an array of ButtonLeds
void shuffleArray (ButtonLed arr [], const int size){
    for (int i = 0; i < size - 1; i++){ // iterates through array except last element
        int j = random(0, size); // generates a random index from (0 to n-1) inclusive
                    
        // swap current index with random index
        ButtonLed t = arr[i]; 
        arr[i] = arr[j];
        arr[j] = t;
    }
}

ButtonLed getButtonPress (ButtonLed arr [], const int size){
    bool pressed = false;
    ButtonLed  pressedButton;
    while (!pressed){ // loops until a button was pressed
        for (int i = 0; i < size && !pressed; i++){ // !pressed allows early out
            if (digitalRead(arr[i].buttonPin)){ // one of the six buttons was pressed
                pressed = true; // exit both loops
                pressedButton = arr[i]; // stores which button was pressed
            }
        }
    }
    return pressedButton; // return the pressed button
}



void setup() {
    randomSeed(analogRead(A0));
    // This is how you set up the leds for output
    pinMode(button1.ledPin, OUTPUT);
    pinMode(button2.ledPin, OUTPUT);
    pinMode(button3.ledPin, OUTPUT);
    pinMode(button4.ledPin, OUTPUT);
    pinMode(button5.ledPin, OUTPUT);
    pinMode(button6.ledPin, OUTPUT);

    // This is how you set up the buttons for input
    pinMode(button1.buttonPin, INPUT);
    pinMode(button2.buttonPin, INPUT);
    pinMode(button3.buttonPin, INPUT);
    pinMode(button4.buttonPin, INPUT);
    pinMode(button5.buttonPin, INPUT);
    pinMode(button6.buttonPin, INPUT);
}

void loop() {

    // This array is of type ButtonLed our newly created data type
    ButtonLed questionNumberArray[] = {button1, button2, button3, 
                                       button4, button5, button6}; 
    const size_t n = 6; // array's size

    shuffleArray(questionNumberArray, n);

    
    
    bool guessCorrectly = false;

    // this while loop allows the user to keep trying until they get it right
    while (!guessCorrectly){
        bool correctButton = true; // the user has pressed the correct button
        ButtonLed userSequence [6];      // stores the sequence the user entered
        // lets the user push 6 buttons
        for (int i = 0; i < n; i++){
            userSequence[i] = getButtonPress(questionNumberArray, n);
            delay(500); // delay between button presses
        }

        // check if the user entered the correct sequence
        for (int i = 0; i < n && correctButton; i++){ 
            if (userSequence[i].buttonPin != questionNumberArray[i].buttonPin)
                correctButton = false;
        }

        if (correctButton){ // user entered the correct sequence
            guessCorrectly = true;
            // This will turn on the leds in the correct sequence
            for (int i = 0; i < n; i++){
                digitalWrite(questionNumberArray[i].ledPin, HIGH); // turn on the led
                delay(500); // delay half a second
                digitalWrite(questionNumberArray[i].ledPin, LOW); // turn off the led
            }
        }
    }
}

Edit 1

Edit 2

I also updated the code for which pins the leds are connected to. Remember they're connected to "pins" Not "ports.