Sounds like the GA messed something up.
A couple of weeks ago SO and I were flying ATL-SJD (Cabo) and we were
#1 &
#2 for one seat.
SO got the seat, I did the walk of shame.
We had already been upgraded on our return flights - and those weren't affected at all.
This has happened to us multiple times where we have split up, and it never resulted in your situation. Weird.