Steps to reproduce:

1. Download and import attached project.
2. Open scene: main.
3. In hierarchy, break prefab connection, when dragging B out of A.
4. Duplicate extracted B.
5. Drag&Drop original B to Assets to create a prefab of B.
6. Click on Hierarchy window.
7. Press ctrl + z (cmd + z on mac), three times.

Expected result: GameObject is the same as before, etc: Parent A, and two children, B and C.
Actual result: B gets duplicated on Undo operation.

Regression from: 5.2.4f1