You asked a good question. I tried to solve it three times. The first time, my intelligence dropped. I explained that I was using an old save game. Which I don't recommend. The second time, I tried restarting the game, even deleting previous saves. When assigning Hermione to a specific class each day, the fine print at the bottom states what decreases and what increases. When I rested for a whole day for Hermione, logically, her stats shouldn't decrease. Yet, as you described, her intelligence drops by -3 points each day. I used cheats, so it's possible that something in the game got messed up. The third time, I also started over with a new save game, but without any cheats. And her intelligence didn't drop. Until I reached the very end of the game. And then it started dropping again. I don't know, maybe it's a game mechanic?
As for the belly button ring, it removes for me, but I can't get rid of the cat's tail. Despite removing it, it reappears in the next scene. It's a bit irritating, because I don't know which quest activates it so it can't be removed. I also wonder if, besides the game saves themselves, there's any information about Hermione's appearance stored somewhere. Today I'll start it for the fourth time and be more attentive to see where the problem lies. An option in the menu to reset all settings and delete game saves would be useful.
