How to reproduce:

1. Create a new Project in Unity.
2. Create a 3D object cube.
3. Make it a Prefab by dragging it into the Assets folder.
4. Duplicate Cube in Hierarchy few times and place them around original Cube.
5. Duplicate original Cube one more time and make it as a child of the original Cube in Hierarchy.
6. Click on the original Cube and apply prefab changes in the Inspector window.
7. Notice how the prefab instances get replaced.

Fixed in: 2018.3.0a11 (An error is thrown "ArgumentException: Cyclic nesting detected", as nesting a prefab into itself is not allowed)

Reproducible: 5.2.4f1, 5.3.5f1, 5.4.0b21

Note: The Bug only occurs if it's the same Prefab. If they differ it works fine.