I had this today too. The solution is simple, click the request upgrade/confirm upgrade button and continue. It's somewhere on the page where it shows available. You now have your upgrade shown as confirmed.

However, this does definately make me wonder... are those upgrades now a first come first serve status? For example, someone with a "T" fare could log in to the website when it screws up and confirm the upgrade before the guy with the "B" fare?