I have similar problems with 2 CSL wireless pads of the same model/type. Sometimes they both even connect to the same USB dongle!.
I dont think its any issue of Batocera at least.
The only solution I can find that kind of works, go into Controllers config from the Batocera menu, and swap around the controller INPUT P1 and INPUT P2, or try setting INPUT P1 to the controller you want, and leave INPUT P2 as Default.
Hope that makes sense, Im at work atm so cant remember the exact setting names.