You can see the mummy in the coffin down there, go into the next room and pick something up, when you look at the level where the mummy is you'll see a green ! (it's the sense creature class ability from the mod active on this save) and when you save the mummy will disappear, though you'll be able to bump into the occupied square if you wish.

Dwarf entity was modified to make tombs and not libraries, but the same effect should occur with human tombs even in vanilla, I don't see why this would be related to any mods in place.