To reproduce:
1. Create a new project.
2. Create empty object.
3. Make it a prefab.
4. Select Prefab instance in Hierarchy.
5. Add Animator Component (or any other component).
6. Apply to prefab.
7. Press ctrl+z
8. Change any value in Transform.
9. Apply to prefab.

Actual result: a new instance of a prefab appears in Hierarchy. (sometimes when it appears it becomes disabled)
Expected result:you have the same number of prefab instances in Hierarchy.

Reproducible: 5.3.7p1, 5.4.4p4, 5.5.2p1, 5.6.0b10, 2017.1.0a2