If I free mouse and click the ability icon, it does allow me to upgrade the ability. However, if I try to press tab/alt and then press the ability key, nothing happens. This only happens with Warden and his 3rd ability as far as I know.
I've had the same problem, but not with upgrading.
Just did some testing with Geist, and literally had to rebind "2" to "2" so that I could cast the ability.
I suspect this patch will probably see a lot of binds getting messed up - definitely Sandbox any heroes you've got on priority after any patch to make sure everything still works the way you expect