There are genuine situations that the score suggestion does not handle correctly. See also this thread: Automatic scoring
Your case looks pretty clear to me. There are no leftover prisoners or anything that could confuse the suggestion algorithm.
Maybe one of you accidentially turned the territory to neutral in scoring?
Anyway, it is the responsibility of both players to check the score before you click “accept”. Only accept the score if it is correct, and don’t leave before both players have accepted and the scoring is complete (otherwise you might lose by escaping).