I had the same problem last week. In my case, EXP desk could not solve the problem, and I was transferred to aa.com website support staff. According to them, the problem is caused by the system trying to read (and check me in to) my outbound flight.

- Outbound flight arrived at SFO at 11:55am
- Return flight scheduled to depart SFO at 3:30pm the following day
- Online Check-in attempts made at around 10:30pm and 1:30pm

They resolved the problem by "forcefully changed the earlier flights to depart after the return flights" according to their words. The entire phone call took about ten minutes.