Recently I was using Nintendont on my Wii U. I own both an official GCN controller (connected) and a Wii U Pro controller (connected). I was playing Capcom vs SNK 2, and for some reason only in this games does the Wii U Pro Controller act strange. It was acting as if the analog stick was being held in a certain direction and navigating really quickly through the menu. I know it's the Wii U Pro because when I disconnect it, it stops. It's odd because but then while navigating the Wii U menu, playing n64 games and even other GCN games it works fine. I had to switch to the Classic Controller Pro and it worked fine.
I wonder if something is wrong with the Wii U Pro controller because I bought it off a seller on eBay that had good feedback and the condition was great. That's the only game I encountered a problem with.