Steps to reproduce this issue:

1. Create a new empty project. (Edit->Project Settings-> Editor->Asset Serialization Mode -> Force text)
2. Set file editor settings to "force text".
3. Add a prefab to the scene
4. Create a new GameObject within the scene
5. Move it above the prefab instance
6. Delete the GameObject, but leave the prefab instance
7. Save the scene
8. Open scene in the text editor
9. Check the value of m_RootOrder
10. m_RootOrder value of 1 instead of 0 for the prefab