Bug is fixed by restarting the game (RELOADING SAVE DOES NOT WORK). Bug seems to only happen if game has been running for a long time.
Probably a memory issue because of the above. When this bug happens, all the store entrances on the bottom floor are also blocked as if in the next phase of the mission, despite me not being there yet. While this bug happens, you also notice the gate makes no sound when being pulled open.
Saving the game in this current state is fine. When reloading save off a fresh instance of the game, the bug will not occur.