I tried talking to Xbox, Mojang, and Microsoft to fix the problem. Xbox told me to contact Mojang, and Mojang told me to contact Microsoft. Also, I searched the web for a solution myself. After much frustration, I found the answer to my problem.
To fix the controller issues with Minecraft VR, you need to run the game, go into the settings option, go to video options, and turn off screen animations. You might want to restart the game if it doesn’t work. After you run it again, your controller should work correctly, with all buttons functional.
So there you go! You can now play Minecraft VR with your Xbox controller. Have a great time – I know I will!