Do you have an input override for this game ? If you open the RetroArch menu and go to Controls/Port 1, what kind of device type does it say it is ?

Please add some more info about your setup, as detailed in https://retropie.org.uk/forum/topic/3/read-this-first.

@Mr_Fix_It Thanks sooo much for this man I've been pulling my hair out for days with these bloody controllers. :)

@caver01 Thanks for you help. This definitely has shed some light on this for me!