Okay so I just learned a little bit more about the situation, even with no controller installed, some games still more on their own. How is that so?
Games this has occured on:
Sonic Generations
Assassin's Creed 4
Battleblock Theater
EDIT I found out why this issue occurred: I had vjoy devices installed so I could use Gamecube Controllers on the PC, I uninstalled those since even without the adapter plugged in, the devices gave some ghost inputs.