How to reproduce:
1. Create a new project
2. Create empty game object and call it "Game Object 1"
3. Drag it to Assets folder so it becomes a prefab
4. Save the scene (Ctrl+S)
5. Create empty game object child of "Game Object 1"
6. Save the scene (Ctrl+S)
7. Select "Game Object 1" and hit Apply so it becomes prefab with a child
8. Save the scene (Ctrl+S)
9. Reopen the project (File -> Open project)
10. Expand "Game Object 1" and notice that additional game object appeared

Workaround: skip the step 6
Not reproducible: 5.2.4p1