Repro steps:
1. Create a new project
2. Create an empty GameObject and make it into a prefab
3. Open the prefab asset
4. In the Prefab Mode create another GameObject and make it too into a prefab (GameObject 1)
5. Duplicate GameObject 1 in the Project Folder (GameObject 2)
6. While Holding ALT drag GameObject 2 from the Project Window onto GameObject in the Hierarchy to replace it
7. Drag GameObject 1 or GameObject 2 into the Scene and observe the Console

Expected: GameObject is Instantiated in the Scene
Actual: An error pops up in the Console

Reproducible with: 2018.3.0b2, 2019.1.0a1

Fixed in: 2019.1.0a4
Backported to: 2018.3.0b7