I'll echo all the other posters above. Duplicate room allocations happen all the time. Personally, it happens to me (either someone coming in or me busting in on someone else) at least a couple times a year. Front Desk clerks are not perfect and, given the most common reason for double allocating a room, neither are their coworkers.

I always presume I have diminished security whenever in a hotel. If I leave something out, I'm taking a chance that any hotel employee or another guest could steal it. Plan accordingly.