I just started this game yesterday and thought the control scheme was ridiculous for controllers. I'm using an Xbox One controller and, even though the in game controls said it was RT to attack, LT is what caused me to attack. I went into Big Picture mode on Steam here and made up my own control scheme, reversing RT and LT (until they hopefully fix it or allow in game button mapping), and switched around some of the face buttons so it feels like Oblivion (Y to jump, A to use, etc).

I'd recommend going into Big Picture mode (that's how they better optimized controller usage anyway) and fiddle with some of the mapping. If you're still having problems, like that odd pop up, it might be your controller or Steam is being picky, not sure how to remedy that, personally.