Once I sat next to a pilot on a TATL flight in BF who was not working the flight, but needed for the flight back -- the flight back was the length of time required for 3 pilots but the flight over was not. He told me that "normally" they give the non-working pilot three seats in coach -- it is part of their contract. But if coach is full, they will move him up to BF, which is what happened in the case where I sat next to him, as that is the most cost efficient thing for them -- to sell the three coach seats rather than an upgrade to BF. He said in such a case, a PAX loses an upgrade. If there was a change in aircraft, it sounds to me like that is what was going on, they were freeing up the non-rev's three seats to fit in the coach PAX and giving him or her the BF seat.
It could also be that the GA was just being nice to the non-rev and of course that would be illegal. And the GA certainly was extremely rude to you by not explaining to you what was going on which looks suspicious.