My ps3’s are wireless and work with all the emulators so far. I assume that you went through the setup for each controller in retropie_setup.sh? I don’t turn on my controllers until emulationstation boots. The only app that I haven’t gotten them to work in is Kodi.
Some games will not respond to controller input if you have your controller set to analog or standard in the F1 libretro menu (depending on the game). I would recommend switching this setting and see if anything is detected.
Look at 5:43 in the video below to see what I mean if unsure. It also goes over controller config if you haven’t done that.