Steps to reproduce:

1. Create new project
2. Add cube to scene
3. Open timeline window and create timeline for cube
4. Exit preview mode and drag cube to project window to create a prefab
5. Back in hierarchy, do some changes to Cube
6. Enable preview mode in timeline and notice that Apply and Revert prefab management buttons are disabled - expected
7. In top menu, click GameObject > Apply Changes To Prefab and notice that it's possible to apply changes

Expected result: Apply changes to prefab menu item is disabled and in sync with Apply button in inspector

Reproduced with: 2017.1.2p2, 2017.2.0p1, 2017.3.0b7, 2018.1.0a3