Advice to the OP:
All of the other direct flights for April 29 have 5 or more F seats available on that day with the exception of two flight (AA 510 has none and AA 350 has two) If a seat in F is important to you, pay for CFC to an earlier or later flight.
As to why your flight may be sold out, there are many possibilities that could solve the mystery...most of them will be or have already been mentioned here. Yes, it's a bummer when this happens, but our EXP upgrade benefits are a privilege, and not a guaranteed given.