GoldenEye is capable of using both GameCube controllers and Wii Remotes at the same time. If you have a physical controller set to emulate both a GC Pad and a Wii Remote concurrently, the game will use both inputs and the physical controller will operate both player 1 and player 2 at the same time. To fix, disable one of the emulated controllers or move one of them to a second physical controller.