How to reproduce:
1. Create new project
2. Add Cube to scene
3. Make prefab of Cube by dragging to to Project view
4. Spawn multiple instances of the Prefab by dragging it from Project view to Hierarchy
5. Delete the Prefab, in prompt select Delete
6. Drag starting Cube from Hierarchy to Project view
7. \[Issue 1] Notice how all previous instances of Cube changed their names
8. Undo a few times past Drag action
9. Redo those Drag actions
10. \[Issue 2] Notice how Cube instances in Hierarchy have duplicates now.
11. \[Issue 3] Try deleting some of the old instances and error pops up (Children of prefab instance cannot be deleted or moved, needs to be unpacked first) - Unpack option is not available for those instances
12. \[Issue 4] Some instances also throw (the Prefab asset is missing. You have to unpack the Prefab instance to be able to create a new Prafab) window, unable to delete them in any way
13. \[Issue 5] Repeat step 5-9 and try deleting some Cube instances, error will be thrown (Cannot destroy GameObject that is part of a prefab instance)
14. \[Issue 6] Enter Play Mode and observe console (Can't destroy Transform component of 'Cube'. If you want to destroy the game object, please call 'Destroy' on the game object instead. Destroying the transform component is not allowed.)
15. \[Issue 7] Repeat step 13 by hold-redoing these changes and Editor crashes

Reproduced with: 2021.2.0b10, 2022.1.0a7
Does not reproduce with: 2021.1.20f1