I don't know squat about airline ticketing systems in particular, but in general large electronic systems frequently keep the same data stored in multiple places.

So, hypothetically(!!!!), the system that backs the website might have a copy of the seats available, while the payment system keeps a separate copy. The two systems have to frequently communicate to stay in-sync, but this is not an instantaneous process.

If you have something happen on one system and then an error occurs when making the change in the other system, you can wind up with a disagreement that takes a while to get ironed out. It happened to me one time when I was attempting to modify my reservation. While trying to pay the change fee, my CC was denied due to possible fraudulent activity. My itinerary showed the change but the ticketing system was unaltered and my card un-charged.

(To add insult to injury in that case, because my itinerary was already "changed", Delta wouldn't re-process the transaction. When I went to check-in the next day the system wouldn't allow me because, technically, I never paid my change fee. The check-in teller had to blank out everything; in the meantime, the ticket had increased in cost by about $200 -- a difference I wound up eating...)