counter is off in program

I have to write a program for my class.

The instructions are

Your program will choose a random 4 digit number as the secret number.
Your program must prompt the user to enter a 4 digit number as their guess.
The program will respond with a message indicating how many of the digits in the user’s guess are the same as the digit in the same position in the secret number.

For example, if the secret number is 3749, and the user’s guess is 9753, then the program would respond with the message You matched 1, because only one of the digits (the 7) in the user’s guess is the same as the digits in the same position in the secret number.

The program will allow the user to continue to enter guesses until they guess the correct secret number.
After the user has entered the secret number, the program will output a count of the total number of guesses the user took to find the secret number.
Then the program will ask the user if they would like to play again. If the user answers “yes”, then the program will choose another random 4 digit number and play continues as described above.

	public static void main (String[] args)
	{
		Scanner input = new Scanner(System.in);
		Random random = new Random();
		
		System.out.println("----- MASTERMIND -----");
		System.out.println("Guess the 4 digit number!");
		

		boolean keepGoing = true;
		
		while (keepGoing = true)
		{
			String secretNumber = String.format("%04d", random.nextInt(10000));
			int guessCount = 0;
			int matchCount = 0;
			while (matchCount != 4)
			{
				System.out.println("Enter your guess: ");
				String userGuess = input.nextLine();
				guessCount++;
				if (userGuess.substring(0,1).equals(secretNumber.substring(0,1)));
				{
					matchCount++;
				}
				if (userGuess.substring(1,2).equals(secretNumber.substring(1,2)));
				{
					matchCount++;
				}
				if (userGuess.substring(2,3).equals(secretNumber.substring(2,3)));
				{
					matchCount++;
				}
				if (userGuess.substring(3,4).equals(secretNumber.substring(3,4)));
				{
					matchCount++;
				}
				System.out.println("You matched " + matchCount + " digit/digits.");
				if (userGuess.equals(secretNumber))
				{
					System.out.println("Congratulations! You guessed the right number in " + guessCount + " guess/guesses.");
					System.out.println("Would you like to play again? Enter Y for yes or N for no.");
					String keepGoingYesOrNo = input.nextLine();
					if (keepGoingYesOrNo.equals("N"));
					{
						keepGoing = false;
					}
				}
			}
		
		}
	}

For some reason the matchCount is always 4 once the program runs even when the numbers don't match.
I thought the code under the if statement would only be executed if the condition is true but for some reason it runs it anyways.

You have semicolons after your if statements making them useless. The format should be like this:

if (userGuess.substring(0,1).equals(secretNumber.substring(0,1))) {
matchCount++;
} 

But also as the program is currently written, matchCount will keep increasing even if they duplicate numbers. So if the number was 1234 and the user guesses 2222 then 2223 matchCount will be two. I recommend setting boolean values for digit1, digit2, digit3, and digit4. When the digit is guessed, set the value to true. Only run each if block if digit[x] = false.

Edit: After some trial and error I made the program as reliable as possible. Before, matchCount would keep increasing even if you repeated the same digits, so to prevent this I implemented some boolean values.

Furthermore, if a digit was correctly guessed but then not guessed in following attempts matchCount would remain the same, so I wrote another set of if statements to decrease matchCount in this event. I also fixed some other minor issues within the code including resetting matchCount when replaying and also successfully ending the program when a user does not want to play. Let me know if you have any questions! Here is the final code.

public static void main (String[] args)
{
Scanner input = new Scanner(System.in);
Random random = new Random();
System.out.println("----- MASTERMIND -----");
System.out.println("Guess the 4 digit number!");
boolean keepGoing = true;
boolean digit1 = false;
boolean digit2 = false;
boolean digit3 = false;
boolean digit4 = false;
while (keepGoing = true)
{
String secretNumber = String.format("%04d", random.nextInt(10000));
int guessCount = 0;
int matchCount = 0;
while (matchCount != 4 && keepGoing == true)
{
System.out.println("Enter your guess: ");
System.out.println(secretNumber);
String userGuess = input.nextLine();
guessCount++;
if (userGuess.substring(0,1).equals(secretNumber.substring(0,1)) && digit1 == false)
{ //if the first digit is correct and hasn't been guessed already, matchcount increases
matchCount++;
digit1 = true;
} 
if (!userGuess.substring(0,1).equals(secretNumber.substring(0,1)) && digit1 == true)
{ //if the first digit is incorrect but you previously guessed it, matchcount decreases and digit1 is set to false
matchCount--;
digit1 = false;
}
if (userGuess.substring(1,2).equals(secretNumber.substring(1,2)) && digit2 == false)
{
matchCount++;
digit2 = true;
}
if (!userGuess.substring(1,2).equals(secretNumber.substring(1,2)) && digit2 == true)
{
matchCount--;
digit2 = false;
}
if (userGuess.substring(2,3).equals(secretNumber.substring(2,3)) && digit3 == false)
{
matchCount++;
digit3 = true;
}
if (!userGuess.substring(2,3).equals(secretNumber.substring(2,3)) && digit3 == true)
{
matchCount--;
digit3 = false;
}
if (userGuess.substring(3,4).equals(secretNumber.substring(3,4)) && digit4 == false)
{
matchCount++;
digit4 = true;
} 
if (!userGuess.substring(3,4).equals(secretNumber.substring(3,4)) && digit4 == true)
{
matchCount--;
digit4 = false;
}
System.out.println("You matched " + matchCount + " digit/digits.");
if (userGuess.equals(secretNumber))
{
System.out.println("Congratulations! You guessed the right number in " + guessCount + " guess/guesses.");
System.out.println("Would you like to play again? Enter Y for yes or N for no.");
String keepGoingYesOrNo = input.nextLine();
if (keepGoingYesOrNo.equals("Y"))
{
keepGoing = true;
matchCount=0;
guessCount=0;
} else {
System.out.println("Thanks for playing!");
System.exit(0);
}
}
}
}
}

First of all, I think you can change the code to this and it is easier to maintain and it is more readable

 public static void main (String[] args)
{
Scanner input = new Scanner(System.in);
Random random = new Random();
System.out.println("----- MASTERMIND -----");
System.out.println("Guess the 4 digit number!");
boolean keepGoing = true;
while (keepGoing = true)
{
String secretNumber = String.format("%04d", 
random.nextInt(10000));
int guessCount = 0;
int matchCount = 0;
while (matchCount != 4)
{
matchCount = 0
System.out.println("Enter your guess: ");
String userGuess = input.nextLine();
guessCount++;
for(int i = 0 ; i < secretNumber.length() ; i++){
if(secreetNumber.charAt[i] == userGuess.charAt[i])
matchCount++;
}
System.out.println("You matched " + matchCount + " 
digit/digits.");
if (userGuess.equals(secretNumber))
{
System.out.println("Congratulations! You guessed the 
right 
number in " + guessCount + " guess/guesses.");
System.out.println("Would you like to play again? Enter 
Y for yes or N for no.");
String keepGoingYesOrNo = input.nextLine();
if (keepGoingYesOrNo.equals("N"));
{
keepGoing = false;
}
}
}
}
}

And reset matchCount after each guess

Empty if blocks

The semicolon at the end of the ifs closes them and the block next to them is executed no matter what. Fix:

            if (userGuess.substring(0,1).equals(secretNumber.substring(0,1)))
{
matchCount++;
}
if (userGuess.substring(1,2).equals(secretNumber.substring(1,2)))
{
matchCount++;
}
if (userGuess.substring(2,3).equals(secretNumber.substring(2,3)))
{
matchCount++;
}
if (userGuess.substring(3,4).equals(secretNumber.substring(3,4)))
{
matchCount++;
}

matchCount should be 0 at each iteration

If you happen not to guess the full number, but at least one of your digits are correct, then matchCount will be a strictly positive number. Since you do not set it to 0, the matchCount will behave in the wrong way. You need to reset it, like

            if (userGuess.equals(secretNumber))
{
System.out.println("Congratulations! You guessed the right number in " + guessCount + " guess/guesses.");
System.out.println("Would you like to play again? Enter Y for yes or N for no.");
String keepGoingYesOrNo = input.nextLine();
if (keepGoingYesOrNo.equals("N"));
{
keepGoing = false;
}
}
else
{
matchCount = 0;
}