I am not sure if you are still having the same issue, but I was experiencing the same thing after the latest update. I was able to fix the issue in the input settings by setting throttle, frameskip dec, and frameskip inc to ‘none’ (which can be achieved by hitting esc). For some reason when hit joystick directions I was randomly registering F## keyboard presses as well. I noticed this when binding some other controls. Not sure why, but those options above are tied to f8, f9, and f10 and seemed to be causing the problem.

I hope this helps.

On RetroArch it's q and w - but please try and be more specific as RetroPie consists of many components that accept input. https://retropie.org.uk/forum/topic/3/read-this-first