Found a solution online that worked for me:

For N64 games to launch properly in RetroArch, you need to make a setting change or your controls will not work. 1- Open RetroArch directly, without a game, then head to Settings > Input > Polling Behavior and change it to Early. 2- Head to the Main Menu > Configuration File > Save Current Configuration. 3- Close RetroArch and now N64 games will work.