Reproduction steps:
1. Open the attached project (testing1.zip);
2. Open the "islandscene.unity" scene;
3. Try to change settings to Tree object (World->StaticObjects->Tree);
4. Observe that changes are applied on all Tree objects;

Expected results: Each Tree prefab can have different settings;
Actual results: The change is applied to instances of the Prefab.

Note: This issue appears even if you: add a child object to break the prefab, remove a child to break it, manually break with GameObject menu or try making multiple generations of prefabs.

Reproduced on: 5.3.5p8, 5.4.3f1, 5.5.0f3, 5.6.0a5.