Twice in the last few months on UX flights out of SFO, I've had GAs not clear the upgrade list. Once, the GA just didn't clear it at all (I was #1 on the list, so the seat would have gone empty if I hadn't mentioned it to a FA) and once she cleared people manually, moving them up from Y but not processing it in the system (so F was full, but the system still showed empty seats). But, I've never had it happen on a mainline flight.
Tough to say which was the case here. The Upgrade tab right now shows that F was fully booked, but only 6 of 8 were checked in. So, probably two people were no shows and the GA didn't then clear the list. Either those seats went empty, or he/she cleared the list manually (though you should have been one of the people moved up) or possibly shenanigans.
I did write in the second time it happened to me and got some courtesy miles, but I had all the facts and I know for sure I should have gotten an upgrade and the GA upgraded someone else (either by mistake or intentionally). My new SPO out of SFO on UX flights is to wait to board until the end, if the list hasn't cleared. I'll then ask the GA about the list -- at least then they know someone is paying attention.