I also noticed these bugs (all of them exept the clipping). But I want to add that upon reloading the game I could not enter the last dorm door anymore (I could not find the key card anymore either, so it broke the game for me)
I happened to find that one missing card, dunno where exactly but I did, skipping the one in the dorm, and stuck once again because couldn't open the chamber cuz of that dorm card.
