So far I've found two scenes I haven't completed. "Return" on day 4, temple, and "Giving Up" in other, einzbern castle. I tried playing through them in scene selections, but the play date wasn't updated, and my percentage didn't go up. As far as I know there isn't any way to go back to those scenes through playing normally. Currently stuck at 99.2%

Yes I've completed the "Flip-flop 3" event on day 4, and also answered all the quizzes correctly