It happens because airlines won't always give you an assigned seat when you book They block certain seats for elite FF members and others, including airline staff. If an elite flyer calls 48 hours out and buys a seat at full price, they want a prime seat available for that person.
Here's an example. On February 12th, we bought three r/t tickets on AA from STL > ORD, for the dates Apr 3 and 14th. I was told that there were no open seats left on the plane for the outbound leg; that although we had confirmed reservations, that the system would not allow seats to be assigned for the flight. I was given seat assignments for the inbound segment, and told to keep calling back as I got closer to departure, that there were about 40 seats left unsold, but that there were blocks on them, and the blocks on the seats would "probably" be lifted as we got closer to the flight date. I called weekly, and was told weekly that they hadn't been released. By the final week, I was calling daily, and again, sorry, they haven't been released. When we got to the airport (3 hours early) we used the kiosk to get boarding passes, and the remaining seats were finally available for selection. Nothing there but single seats.
It happens all the time, and the cheaper your fare, the more likely it is, because higher-priced fare classes override the seat blocks. I'm really good a finding the cheapest fares available, so I get blocked rather often.
BTW, I don't think that AA does this any more often than other carriers. It just happens that they have nearly a monopoly at my airport, so I happen to fly them more often than the others. I prefer SWA, but many of my more frequent destinations are places that SWA doesn't service.