We have a model where multiple doors have been placed in a wall which automatically generated associated openings. But if we delete some of the doors, the respective openings remain instead of being deleted along with the door. We also noticed that if we modify the size of the doors the openings do not change, and if we move the doors the openings do not move with them.
Doors include a "rough opening" component which is simply a 2D shape the size of the door itself, and that shape is used to auto-generate the opening via a Feature cut. However, in all of these cases there were actually two openings in the area of each door that can be seen by using the Building Element Info tool and switching to the Features tab.
If you deactivate each feature one at a time you can visually see which opening is sized appropriately for the door.
The opening generated by each door is still intact which is why when copying that door along the wall a new opening is auto-generated, or when deleting the door the associated opening is removed as well, leaving behind the additional opening/feature (if not deactivating or deleted).
If you were to delete the extra feature from the wall instead, any operation performed on the door (such as delete or move) will result in no extraneous opening remaining.