I’ve been having this issue too, specifically with rooms that could function as Department Head Living Quarters OR regular Living Quarters. I think the room gets stuck in a half-half state, or double-room state, where it is both and neither at the same time.
is it those same rooms for you?
soecifically, Theresa’s, Jake’s (which will also be Lupe‘s room in my playthrough), and the central security office on the second floor all get stuck like this.