I think it's a problem with doors that are not "online" whether it is due to the systems age or cost. I haven't really worked with properties that weren't online but I know for check outs, the system initiates a cancel command telling the door that the card is no longer valid. For a door/system that isn't online, you must physically create a cancel card and go to the door telling it that the card is cancelled. It's designed so that the card holds all the rights and if the system is offline (or there's a network outage), the doors will continue to work.

I have a feeling that this is what happened.