@lex3001 Please excuse the question, but are you really sure about the ghost inputs only happening in the Arcade menu? I ask because It sounds rather strange. Did you wait long enough in all of the menus to rule out mere coincidence of it happening only in the Arcade menu?
You can test a controller for ghost inputs out of Emulation Station by pressing F4 (you'll land in Retropie's command console) and entering this command:
jstest --event /dev/input/js0Any inputs coming from the device will be listed while the command is running. You may have to change js0 to the device name of your controller, e.g. js1, js2 etc. You can end the test by pressing ctrl+c and return to Emulation Station with the command exit.
As for solutions for ghost inputs from bluetooth controllers, I fixed those that came from my Qumox Wii U Pro controllers by using a Mayflash Wii U Pro wireless adapter instead of the Raspberry Pi's own bluetooth to connect them. That got rid of the ghost inputs for good.