Happened to me recently, TPA-ORD, confirmed upgrade T-24 or so, then did SDFC with 3 seats up front showing available on EF but I ended up in coach (9E or something terrible).
Did it through the app, too.
Asked at the gate if I was eligible for an upgrade (I’m EXP, usually #1 or #2 at worst on the list) and they just shrugged.