Please add some info about your setup, as detailed in https://retropie.org.uk/forum/topic/3/read-this-first and use the correct category for your posts (I moved your post to the support category, where it belongs).
The hotkeys are automatically added when you configure your controller in EmulationStation, can you post the controller profile generated for your controller, located in /opt/retropie/configs/retroarch-joypads ? There should be a .cfg file named after your controller, which contain the configuration of the controller.