Great answer, in your answer are the response of why this code should be replace by not reivent the wheel and use Integer.parse and avoid these lines that does not gather unknown inputs. it's just my opinion and your code is ok.

and the check for length can be done before the loop

exactly, strange it got so many 'clever' votes.

So close ;)

Looks like a C program. There is a stack in Java, use it. Guess it doesn't handle "(x)".

This doesn't work - try {'n', 'w', 'n', 'w', 'n', 'w', 'n', 'w', 'n', 'w'} as input.

Yes, we can solve that by doubling array + liniear hashing for example. But I think it is okay for sake of possible solution.

This will fail when there are hash collisions.

This case fits description and will brake a lot of exisitng solutions.
Case of shuffling numbers is not covered. I think below test case will cover it.

@Test
public void test5() {
assertEquals("", 2, new BrokenSequence().findMissingNumber("5 3 4 1"));
}

Will crash on empty string