I have had this issue with connecting flights. Looking at a DCA-JAX-AUS (unconventional but only way with availability) routing next year.
- On AA.com, DCA-JAX-AUS comes back with "U" availability for 2 seats
- If I search ExpertFlyer (which I know is unreliable for AA connections in general), it again shows 2 seats in U
- However, if I search ExpertFlyer one leg at a time, it shows 0 seats DCA-JAX, and 7 JAX-AUS
- The BA site matches what ExpertFlyer returns on a segment-by-segment basis (nothing DCA-JAX, nothing DCA-JAX-AUS, but will show availability JAX-AUS only)
AA availability is very, very, very sparse nowadays.. the best option is to use AA miles (if you have any), book one of the undesirable connecting flights it will typically offer on miles, then hope for a schedule change to get what you really want.