Try to reset the controllers.
While you are in emulationstation press the F4 to jump to the terminal window, and type :
sudo ~/RetroPie-Setup/retropie_setup.sh
Then choose :
Manage packages => Manage core packages => emulaionstation => Configurations / Options => clear/Reset emulationstation input configuration
After that, restart the system and it will ask you to configure again your controllers.