Steps:
# Create a Cube 
# Convert it to Prefab Instance
# Remove BoxCollider
# 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