How to reproduce:
1. Open attached project and in any scene navigate to the "Hierarchy" window
2. Create a new empty game object
3. Drag and drop the game object to any folder inside "Assets"
4. You will either see the errors described above or directly get the crash
5. If the Editor doesn't crash, delete both the prefab and the game object from the hierarchy and repeat steps 2 and 3.

Not reproducible: 5.3.4p4

Reproducible: 5.3.4p5, 5.3.6p4, 5.4.1f1, 5.5.0b2