How to reproduce:
1. Open the attached project ("case_1174963-PrefabBugTest") using the EnvIronman VM (optional) (more information in Edit)
2. Drag the "TestPrefab" prefab to the scene
3. Set its transform position to any value (different to default)
4. Add two more instances of the same prefab in the scene
5. Set one of the newly added prefab instances to be a child of another newly added prefab instance
6. Click on the parent prefab and apply changes
7. Inspect the original prefab's newly created child transform position

Expected results: Transform position matches other prefab's position
Actual results: Transform position has an offset

Reproducible with: 2017.4.31f1
Couldn't test with 2018.4 and above as they are using the new prefab system