"Destroying object multiple times" error message appears while applying removed component to prefab asset

Steps:

1. Create a Cube 
2. Convert it to Prefab Instance
3. Remove BoxCollider
4. Component context menu: "Removed Component -> Apply to prefab 'Cube'"

Editor window is minimized.

"Destroying object multiple times. Don't use DestroyImmediate on the same object in OnDisable or OnDestroy." error message appears in Console.

Note:

• Also repro when applying added GameObject with right-click. 
• Also repro with Layout -> Save Layout..
• Right-click in Project Browser -> Create -> Text -> Sprite Atlas