Are you using 3.0 or 2.6?

If 2.6, have you completed the retroarch joyconfig? No? Do this:

Press F4 to exit ES

sudo chown pi /opt/retropie/configs/all/retroarch.cfg (only once)

cd /opt/retropie/emulators/retroarch/bin

sudo ../retroarch-joyconfig -j 0 >> /opt/retropie/configs/all/retroarch.cfg

For the 2nd controller use -j 1 >> and so on…