Steps:
1. Create a new project
2. Add GameObject and convert it to prefab
3. Duplicate prefab instance
4. Parent one instance under another
5. Select the root and open Overrides window
6. Select Added GameObject and Revert it from Comparison window
==>
MissingReferenceException: The object of type 'GameObject' has been destroyed but you are still trying to access it.
Your script should either check if it is null or you should not destroy the object.

Regression from: 2021.2.0a10

Please, take a look into attached movie