An update, I found another one of those crystals with the bug collision on the right, but this time in the seal of water in the top of the left room from the central room with the large arcane symbol on the floor and the door purpleish you need two pull to levers to open.
I also found in the jelly girl’s room in Lady Lake, the lamp in the left of the room above the couch also has no collision. Man, I’m just a magnet towards the stuff lol
It might be a coincidence, but the fact these crystals had the same kind of bug and both in the water, while the land ones were right, makes me think this might be a bit more of a widespread issue. It’s probably not, but I’ll be on the lookout for any more of those kinds of crystals to test out just in case.
Still having a great time with the game by the way.