Yes it can happen than one factor is zero (or both...). Non-negative meaning ">=0". I tried your solution and the problem comes when an element is zero because in this case the condition "P = A ** 2 + B ** 2" is not satisfied by your return. It is possible that you have an issue when seeing if a big integer is a perfect square or not.
Allow me to add that your code doesn't follow the right way to find an answer in all cases. Cheers and good luck.

The tests fail when one of returned numbers is 0, while description says the answer needs to be non-negative.

As a temporary workaround you can try to return such pair, where none of the numbers is 0. For example, tests fail for:

Input: [3, 2, 5, 5, 4, 2, 6, 6, 9, 3, 3, 2, 3, 7, 2, 3, 4, 9, 6, 7, 3, 8, 8, 7, 6, 3, 6, 6, 4, 4, 5, 3, 9, 8, 3, 9, 2, 2, 6, 6]
Output: [38575890503412110, 0]