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

By repeating steps 7 and 8 you can get as many of the same Components on the object as you want.

Expected result:you have the same number of components.
Actual result: you get more of the same Component on your prefab.

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