Steps to reproduce:
1. Open the attached project
2. Open the Assets/init.unity scene
3. Play the scene
4. Click on Menu bar -> demo -> load_prefab
5. Open Profiler. Review detailed info of GameObject. You can see cube and sphere
6. Click on Menu bar -> demo -> unload. It will call unloadUnusedAsset
7. Open Profiler. Review detailed info of GameObject. Sphere has destroyed but Cube was not

Actual result: Sphere has destroyed but Cube was not
Expected result: Cube and Sphere should be destroyed

Reproduced with: 5.5.4p1, 5.6.2p1, 2017.1.0f2, 2017.2.0b1