How to reproduce:
1. Create a new project
2. Save the scene
3. Drag and Drop Main Camera from Hierarchy to project folder so it becomes a prefab
4. Reopen the scene and notice that Unity doesn't prompt user to save the scene
5. Also if you after creating a prefab save the scene (Ctrl+S) and then reopen the scene, you can notice that it hasn't been saved
6. If the same scene later is used with earlier versions, the same issue exists

Not reproducible: 5.3.1p1