Originally Posted by fastair

My guess (and it is only a guess): Agent scanned all 3, then in order to get his/her passenger count, to match the number of passengers shown on the computer, he/she deboarded that seat (most likely to print paperwork for the crew and for weight/balance.) He/she then either failed to recheck that person in so ticket showed used, or another agent (were there 2 working the trip?) saw the open seat and moved someone to it or onloaded a standby into it (after all, people want windows instead of centers.)

So my theory is either poor communication between mulitple agents, or a forgetful agent (if he/she then reassigned it out without remembering it was in use.)

I've seen this happen before, I'm sure I'll see it again sometimes. Rare, but not unheard of.