@Kristopherson05 I still need more information. How did you configure the controller? Did you use the autoconfigure in Emulationstation? Did you edit the configs manually? Where is the copy of your configs for us to inspect?
You say Joystick? Is it connected via a USB controller, if so which one? An Ipac? if so a 2 or 4? or even a mini-pac? or maybe a Xin Mo.......each one presents it's own challenges.
Maybe all this is sorted and you are using MAME. Maybe it's not a retroarch version so you could have hit TAB and messed up things?
In order to help, I suggest that you follow this:
https://github.com/retropie/retropie-setup/wiki/retroarch-configuration
Not sure that it is possible to provide any further answers at this point without speculation.