How to reproduce:
1. Open QA-Supplied project (link in Edit)
2. Open Scene in Assets -> 00_Scenes->outdated->PrefabBug
3. In the Hierarchy window, select level (disconnected and wrong hierarchy)->PolyP and drag it into the Project window to create a Prefab
4. Ctrl + z to undo

Expected: Hierarchy text is blue (since it is a prefab now), Inspector doesn't show a "disconnected" warning, opening it from Hierarchy opens the prefab.
Actual: Hierarchy text is grey, Inspector shows a yellow "disconnected" text, opening it from Hierarchy opens a different prefab

Reproduced in: 2019.3.0a3, 2019.3.0b11, 2020.1.0a13
Not reproduced in: 2017.4 (old Prefab system) 2018.4.13f1, 2019.2.13f1, 2019.3.0a1, 2019.3.0a2