Then the translation would be "Pojken äter inga äpplen.", since you can kind of count the apples: No apples, one apple, two apples. The boy might eat apples at another occasion, but not this time.
To get the gist of not eating apples at all (probably at any time), you would say "äter inte äpplen" = "does not eat apples".
The boy does not eat apples. is the preferred translation so it should definitely not complain about that. Either you had some typo without noticing or there is a bug. If it doesn't accept the main translation again, for you or anyone else who reads this, please grab a screenshot so we can report it properly.