ive found a few of them so far
ill list what ive found (so you dont get stuck)
there is a few more but i cant remember them right now

-level in the lunar ruins dungeon with the calcobrena dolls//death puppets
if you finish this a second time (killing all the dolls) opening the chest that contains the nirvana rod will cause the game to freeze.
-one of the final floors in this dungeon, a chest in the middle of the room that contains a 'golden apple' is never added to the inventory