According to other Google Search Results, and Forums, UBISOFT has an issue with its mapping of controllers,
I have a Wired Razer Onza, selected use Controller in settings in Game, Pressing B=A, X=B, Menu left control stick click. as for Example,
I would go through all the Issues with this but i want a Fix that I can just paste with out moding, or Have this issue resolved with the Next patch.

In the mean time, the 360 Emulator to remap a controller CBF! but going into game and working out all the bugs, seriously Purchaced the game to play not to Fix an issue such as this? Side question! how hard was this to Stuff up? Great Game and I know issue come up but this is something a 1 day Apprentice would get right