To reproduce:
1. Open project attached by the user
2. Open scene "scene" if not opened
3. In hierarchy window select game object "Prefab"
4. Expand it and place game object "B" above "A"
5. Hit play and notice that order has changed

Expected : After hitting play order won't be changed
Actual : Order changes after hitting play

Reproduced with : 5.4.4p4, 5.6.1p4, 2017.1.0b9, 2017.2.0a4

Note : Happens only when new child game object is added from above.

Fixed with improved prefabs system.

Version 2018.3.0a5 (24a51b984e30)
Mon, 09 Jul 2018 17:22:19 GMT
Branch: prefabs/improved