To reproduce:

1.Download and open attached project
2.Open Scene "Scene"
3.Enter Play mode
4.Exit Play mode
5.Press CTRL+S
6.Click the arrow to view prefab's child objects in the project window

Expected result: Only 2(Cube and Sphere) Child objects are shown.
Actual result: All individual components of child object's are shown separately.

Fixed in: 2018.3.0a6

Reproduced with: 5.6.0b3, 5.5.0f3, 5.4.3f1, 5.3.7p2.

Note: Bug appears only when HideFlags.NotEditable property is set to Prefab gameObject. When Play mode is entered again, all separated child object's components disappear, but after saving appears again. Images of expected and actual results are attached.