Using an Xbox controller, the game thinks there are 2 players, assigning p1 and p2 to the same controller. This doesnt effect gameplay but it makes using any menus almost impossible, as either you are clicking twice on something or clicking on two different things at once, so no input or the wrong input. At the moment I have to use the mouse whenever I want to interact with menus and then go back to controller for gameplay.

On Steam forums there seems to be a fix for this by choosing to allow steam overrides in prefs, but there doesnt seem to be a similar fix for the GOG version.

Hey good news, you can actually use Steam to launch the GOG version by adding it as a non-Steam game, then in properties you can use the Steam Input override solution to fix the issue.