To reproduce:

1. Open the attached project
2. Open SampleScene
3. Select the Video Player Game Object in the hierarchy
4. Change any option in the Video Player Component in the Inspector
5. Go to the Overrides drop down in the Inspector
6. Select the Video Player Component
7. Close the overrides popup window.
8. Delete the Video Player prefab from the scene
9. Re-add the Video Player prefab to the scene (this is necessary only for the error message to show up)
10. Enter Play Mode

If one opens side by side diff view 5 times, five errors will appear upon finishing repro steps. The component editor does not seem to be destroyed.

Reproduced on: prefabs/improved, 2018, July 4