To reproduce:
1. Open any project where you have a prefab with child objects
2. Place the prefab object in the scene
3. In the assets, change the child objects name
4. The change is visible in the hierarchy, but not in the project window
5. The change only becomes visible in the project window after the project is saved.

One part of the behavior that is described here as a bug is actually correct, namely that the project view doesn't update directly. When the user changes the name of the child object, he only modifies the prefab instance and not the actual prefab. He needs to hit "Apply" in order for the changes to actually propagate from the instance to the prefab. This will then also apply the change to the other instances of the same prefab in the scene (which haven't been affected by the renaming before either).

However, the fact that the prefab changes are automatically applied when doing a project save would be incorrect. Testing this in Unity 5.0, however, shows that here the behavior is correct as well, i.e. the prefab instance chances are only applied when hitting "Apply" and not when doing a project save.