I got rid of Ghosts Inputs
I managed to get completely rid of ghosts inputs and wanted to share my solution, so maybe it can help somebody.
I had 2 controllers paired with retropie on the onboard BT, a PS4 V1 controller and an 8bitdo. Both had the ghost inputs problem in menus.
Maybe some steps are unecessary; feel free to comment, i'll edit the post if it's wrong.
raspberry switched off.
plug an usb keyboard.
go to the bluetooth settings, and unpair everything.
Once rebooted, exit emulationstation.
with SSL edit config.txt with command line sudo "nano /boot/config.txt"
add "dtoverlay=pi3-disable-bt" at the end. Save and Exit properly. Maybe reboot and check the line is still present after reboot to be sure.
Get an UBS BT 4.0 plug and play dongle, plug it.
Switch on retropie and emulationstation.
Make sure controller are charged.
Pair again your controllers using the keyboard.
Emulationstation should propose you to configure the controller, do it.
Should be ok ! with no ghosts inputs, and a little less lag, depending on the usb dongle quality.
Edit : once paired, my controllers are only used by retropie. Dont expect to be able to use it alternatively with retropie and PS4, or you'll have to re-pair them again.
Edit 2 : if you use ethernet and don't need WIFI, you can also add dtoverlay=pi3-disable-wifi to the config.txt file, some say it lowers latency.