access your autoconfig file for the controller you are using in this folder:
/opt/retropie/configs/all/retroarch-joypads
and then remove all the hotkey references that you don’t want (for example in the following take out all these references except the input exit emulator button and input enable hotkey button
input_save_state_btn = "5"
input_exit_emulator_btn = "9"
input_load_state_btn = "4"
input_reset_btn = "2"
input_state_slot_increase_axis = "+0"
input_menu_toggle_btn = "0"
input_enable_hotkey_btn = "8"
input_state_slot_decrease_axis = "-0"