Yeah, I've seen that happen...Showed up for a recent LGA-DFW flight and was early, so I SDFC to earlier flight since there was a decent Y seat open. End up like no. 3 or 4 on The List with only one seat open. In the process of SDFC, agent mentioned to me that no one would clear because they had a full fare F who is CK that was ticketed on my original flight but wanted the seat on the earlier. Of course, that makes zero sense but it wasn't my seat to lose so I just went on with my day. Ultimately watched the lady who was #1 go up and ask for the upgrade as boarding began only to be told no with the same nonsense explanation.

Anyways, I agree that AA makes it really difficult to make day-of changes after buying any discounted F fare and it can be extremely frustrating!