Did you try first using the sixad driver? I don't think the controller works as a generic bluetooth device. Are the controllers the only bluetooth devices you are using?
I would 1) re-install from scratch, 2) pair any other bluetooth devices you want to use, 3) install sixad from retropie-setup.
After that, simply plugging in the controller once should register it with bluetooth. You never have to actually pair it yourself. After the initial plug-in, hitting the PS button should pair it up, and from there Emulationstation should detect it with no issues.
I'm only suggesting #1 (reinstalling) because I haven't a clue what that message means, and not knowing what you tried, it's probably easier to re-install than attempt to backtrack. #2 is necessary because sixad disables something that bluetoothctl needs (some kernel module I think, I forget), and you won't be able to pair new devices after that.
Once you get this working, before you tinker with anything else, I'd highly recommend saving an image of your card, so that the worst-case scenario is simply backtracking to a working system, not a brand-new installation.