Steps to reproduce:
1. Download 1010932_repro.zip and open "TestScene" scene
2. Select TestPrefab game object (UI->TestPrefab)
3. Press "Regenerate GameObjects" button on TestScript component
4. Observe the position of all the buttons in the Game View
5. Press the Apply button on the "TestPrefab" GameObject
6. Observe that all the button GameObjects have changed position

Expected results: Applying changes to prefab doesn't affect the position of any components.
Actual results: When applying the prefab, the newly instantiated GameObjects are changing their transform positions to match the GameObject they were instantiated from.

Reproduced with: 2018.2.0a3, 2018.1.0b10, 2017.3.1p4,
Not reproducible with: 2018.2.0a3, 2018.1.0b9, 2017.2.2f1
Regression introduced in: 2018.2.0a3, 2018.1.0b9, 2017.3.1p1