Full disclosure: I'm using Kuloslav's Map Revealer mod.
I noticed the last couple of times I've gone into a temple that when I hit TAB to view the map the key item icons don't sit on the correct locations. Case in point:
The icons seem to be two "rooms" too high (and a touch further left than they should be). In-game I have access to everything in its proper place (the entrance is at the top of the upper right room, the wishing well is in the middle of the room south of that, etc.), it's just not aligning correctly on the overview map.
I don't think it's an issue with the mod because I've been using it reliably for the past couple days in Hamlet, and the overview map of the "surface world" is correct. I also don't see this issue while exploring the cricket/ant/whatever nests.
- Start new Hamlet world - Use some sort of "reveal map" console command to complete overview map - Enter a temple (possibly explore a few rooms)