To reproduce:
1. Open attached project
2. Open scene "Scene"
3. In project view select "BadPrefab"
4. Attach a "Deletable" script to the prefab
5. In Hierarchy, select UnityBug, it should have "My Object" set to the prefab
6. Click on the "Delete" box - it deletes the script on the prefab and toggles itself off
7. Undo the deletion - the script is back
8. Reopen unity - the script is gone and "Component MonoBehaviour could not be loaded when loading game object. Cleaning up!" is printed in console