I flew SFO-FRA a few weeks ago and had an empty seat in C next to me, which turned out to be used by the pilot as a crew rest seat. He used it for maybe an hour or a little longer to have dinner and watch a TV show, and then he went back into the cockpit to sleep. It's possible a similar thing happened on your flight, and the FA in coach was moved to an unoccupied crew rest seat. IMHO it's really not worth your time trying to second-guess the ugprade system and whether someone didn't get upgraded who should have.