I've had some issues recently too;

One reservation with 5 PAX allowed me to select some bulkhead row seats. AA later moved the 5 PAX to other seats claiming the bulk heads were for gate check in only. The seats still showed as available so I moved the PAX back and they're still there, go figure.

I often have the situation where the seats show available but can't be selected especially in the F cabin when only 2-3 seats are available and I received a upgrade confirmation within 2 hours of departure.

I've also noticed that when I use the 'check available seats' function for a flight on which I have a seat it sometimes shows my seat as available!! Though I'm sure it's not really available.

Perhaps the little ICONS that they use could be used to illustrate the actual avaialability. Instead of just available, not available, reserved for disabled pax, they could add; reserved for PAX paying F, available for UPGrading PAX, Held for gate check-in, Set aside for the FA's to sleep on, Out of service, Warning RULE 6020 PAX in adjacent seat, PAX with infant in adjacent rows.