This is an unfortunate side effect and there's not much that can be done since both Ultra SFIV and SSF4AE share the same AppID in order to enable network compatibility between upgrade users (those who upgraded from SSF4AE) and full-on USF4 owners (customers new to the series on PC).
I guess this explains why I appear to own some GotY versions of games that I certainly did not upgrade.
Don't trust the smiling penguin! http://backloggery.com/mydogskip93
You guys haven't got Ultra SFIV for free. It upgrades it so you can play against others who have the ultra version, but you won't be able to use the new characters etc. Many games do this, for example world of warcraft upgrades you to the latest version, even though if you haven't bought it you won't experience the new content. Another game that does the same is company of heroes 2, you will have the 2 new armies installed, but can't play as them, just play with other players who have bought the expansion.