That’s about this old issue where you can’t turn around yourself in FPS games (like TyrQuake), or your mouse pointer stops on an invisible wall.
If you can try this retroarch version here (for win x64 only) and tell me if that works for you.
Tell me which version of Windows you’re using. See if that works in menu too if possible, like navigating with glui in a window.
I think Nestopia has a particular problem with mouses though, other cores should be fine.