To reproduce:
1. Open project attached by the user
2. Build asset bundle in project window (right mouse click -> Build Asset Bundles)
3. Open "Source" scene in Source folder
4. Hit play and notice that prefab changes its Y position
5. Open scene "Player" in Player folder
6. Hit play and notice that the same prefab instantiated from Asset Bundle remains still
7. Open timeline editor and notice that there is no track for instantiated prefab

Expected: Prefab instantiated from Asset Bundle should behave exactly the same as prefab which was manually placed to the scene.
Actual: Prefab instantiated from Asset Bundle looses its track in the timeline.

Reproduced with: 2017.1.0b1, 2017.1.0f3, 2017.2.0b2

Note: Instantiating prefab via script with Instantiate() method works as intended.