I don't have those controllers, but had the exact same issue with 2 8bitdo SFC30 controllers: When i 2 player games player 1 would control both players.
The issue was that the controllers were connecting in "keyboard" mode and the d-pad keys in this mode are mapped to the keyboard ctrl keys (presume a computer only normally has 1 keyboard hence both controllers were mapped to the ctrl keys)
The solution was to get the controllers to connect in "joystick" mode and then they worked correctly.
However, they required totally reconfiguring again and I went back to basics to do this and more or less followed this video:
I had to remove the blue tooth pairing and re-pair in this mode.
I reverted the /opt/retropie/configs/all/retroarch.cfg back to defaults and the final solution had NO configuration in here just using the auto map functionality.
Used a default joypad config file from here: https://github.com/libretro/retroarch-joypad-autoconfig/tree/master/udev for my joypad in here: /opt/retropie/configs/all/retroarch-joypads/
And then did the Normal Emulation Station input process (and manually added the hotkeys into the ES_input file)
Matt...