I need to point something out here as I had problems using them over bluetooth.
Not sure if anybody else has the same problem but it been there since I started using retropie a couple of years ago and is still there now.
It does not effect all games but I have noticed it in a few, hogs of war is one that comes to mind.
I use to use 2 normal ps2 controllers via usb adapter and 2 ps3 controllers via Bluetooth for some 4 player fun. The 2 ps3 controllers over bluetooth always use to cause stuttering whilst holding the button to fire your rockets in hogs of war, the 2 wired controllers never did this.
The way that solved this for me was to disable the built in wifi on my pi3, then they worked perfectly.
I now use 4 ps3 controllers via Bluetooth with no problems what so ever now since disabling built on WiFi.
Hope this helps just incase you come across same problem.
Rob