Not sure if the core is the correct spot - but Corpse Killer is always detecting a 2nd controller when in use on MiSTer - this confuses the game and you cant really play it correctly via controller - requires you hopping back and forth between 2 controllers. If I only have 1 Bluetooth controller, or 1 USB controller, or even just use SNAC - it always detects a 2nd controller even though there isn't one plugged in.
Software emulators sometimes require you to disable the 2nd port all together. Not sure if there would be a way to do that, or just have it know that other controllers are not active.
EDIT: Seems if you enable joy 2 to be a menacer in the settings it will still allow you to play with a controller. Odd behavior, but a work around.