- Open scene Game in attached project
- Reparent the airport_placeholder (a prefab instance) to the Directional Light game object
- On the SpriteRenderer component for the airport_placeholder change Order in Layer from 1 to 2 and press the Apply button (to apply changes to prefab)
- Notice that another airport_plaheloder prefab instance gets created in the Hierarchy where the original one used to be and selecting either one of them selects the other (almost like they are the same game object)

This is a regression from Unity 5.1.1f1