I have had an S3 be given my seat my a GA before.
However, this sounds more like a situation I had last year on DL 1285 DCA-ATL. Flight originates at JFK. Since there weren't medallions requesting seats in JFK, a flight attendant in uniform commuting back to ATL rightly took seat. Since she was in seat as "through" passenger, that seat did not show as available for upgrading at DCA. I asked GA about that; he said that once upgraded flight attendant didn't need to give back seat. If I hadn't been already upgraded, I would have been livid. I was considering going to back of plane and finding out who was next on list and letting them know why they weren't upgraded.
It would be interesting to know if the OP was on the second leg of a through flight.
Marc