I think airlines have to do a count just prior to doors closing, to make sure the number of passengers on board = the number of passengers checked in (or the number listed on the manifest).

Could the GA have been lazy, and "upgraded" someone after they already boarded, and then neglected to a) go get that passenger and move them to first, or b) realized they had already boarded and offered someone else the upgrade?

One remote possiblity is that the owner of the first-class coach seat had a companion in coach, and went back to sit with that person (assuming coach wasn't full). Why that person wouldn't tell the FA, or swap with someone in coach, is beyond me, but again, I suppose it's a possibility.