I think I have found the object in the map causing it. When I made some major backend changes to how the map files were read and spawned it added proper collisions in this case the interior just under this area seems to have a bigger hitbox than it looks like it should have. It should be fixable by moving the interior down further.
EDIT: The collisions are for NPCs later down the line so that they (hopefully) don't phase through things when pathing or chasing players.