Had this happen the other night and a few months back too. I've figured out the steps that cause the behaviour.
In gaming mode, I launch discord (but could be any flatpak), then I launch EmulationStation DE and launch a game from within that (via dolphin emulator in these tests). Now in the gaming mode interface, the dpad, face buttons and start+select all send double input. Thankfully it doesn't affect controls within either open app though.
This issue persists after closing these apps until i put the deck to sleep and reawaken. If anyone has any advice or can reproduce this behaviour, please let me know. Thanks.