To reproduce:
1. Open project UnityGameObjectMarkerBug
2. Open Scene
3. In hierarchy select Container
4. In the Inspector select Prefab and then Non Prefab in the Test Script. In hierarchy the GameObject gets highlighted and it's text color changes to white
5. Add Prefab from the project to the scene
6. Select the Non-prefab in the test script. The GameObject's text color changes to blue in hierarchy, which makes it look like a prefab, even though it isn't

The blue text does not reproduce with Version 4.1.5f1