Perm-Missing-Elem: 100% functional score, but only 60% performance
@chillworld is correct in his observation that the issue is related to the int overflow causing the problems in the performance tests.
The more accurate solution to this is to use a long to set the score, instead of an int.
public class Solution {

    public int solution(int[] A) {

        long N = A.length + 1;
        long total = N * (N + 1) / 2;

        for (int i : A) {

            total -= i;
        }

        return (int)total;
    }
}

As for your code, I understand why you have variables with names like N and A, because those are the variable names used in the problem.
Those variable names do not conform to standard Java naming conventions though. They should be meaningful names, and start with a lower-case letter, like sum, and data.
the fact that my code below still uses N is not an indication that it is OK .... Do what I say, not what I do...

Update
Sometimes, the performance tricks in Java can be a PITA.

Whenever you can, declare your variables as final
declare your methods as final
declare variables and for-loop variables as final (if you use the enhanced-for semantics).
addition may, or may not be faster than subtraction.

Using this code:
class Solution {

    public final int solution(final int[] data) {

        final long N = data.length + 1;
        final long total = (N * (N + 1)) / 2;
        
        long sum = 0L;

        for (final int i : data) {

            sum += i;
        }

        return (int)(total - sum);
    }
}

Scores 100%

Update 2 final is not the issue:
public int solution(int[] data) {

    long N = data.length + 1;
    long total = (N * (N + 1)) / 2;
    
    long sum = 0L;

    for (int i : data) {

        sum += i;
    }

    return (int)(total - sum);
}

Also scores 100%