I reproduced this bug in a quick game with "Adda", just with GQ and no other expansion. The game ended with tile count on 2 just the same. I don't consider this bug a big issue, but it can get annoying, if somebody wants to place the abbey on last turn, maybe to check were the best spot regarding the German monasteries is, and then can not place it at all.
Speaking of which: I would rather support a warning message box, if you are going to skip placing the abbey after all tiles have been played. You can argue, that people should watch out, how many tiles there are still to play, but this is a mistake, which will hardly ever occur, when playing actual board game on the table, just like you will never place accidentally a meeple instead of a tower piece on a tower there, an action, which cause a warning on JCZ as well.