Steps to repro:
1. Add a new 3D cube as a GameObject
2. Move it to the assets to make it a prefab
3. Now press undo (cmd + z) till it is removed from the hierarchy
4. Do a redo to create the object

Note that the prefab structure is corrupted in the hierarchy and now we can see a parent container and the child. The label is no longer blue.

Check screencast for more information.

Happens the same on 5.3.4p4 and on windows 8.1 64 bit as well