Ok, in that case, when you run games via retroarch it is processing this file for your controls:

/opt/retropie/emulators/retroarch/configs/USB_Gamepad_.cfg

You can read this by typing
“sudo nano /opt/retropie/emulators/retroarch/configs/USB_Gamepad_.cfg”

Assuming you havent edited
/opt/retropie/configs/all/retroarch.cfg or
/opt/retropie/configs/{systemname}/retroarch.cfg

then the first file above is how it works out its controls.

You can check the file matches your controller buttons with jstest

If it doesnt match, just reconfigure it using the wizard here (or do it manually if you want):
“sudo /home/pi/RetroPie-Setup/retropie_setup.sh”

Then choose
3- Setup
320 – Configure input devices for RetroArch