To reproduce:
1. Create a new scene.
2. Add a UI Canvas, add an empty "GameObject" with "VerticalLayoutGroup" component as a child, add UI Text gameObject as a child to the "GameObject".
3. Make a prefab of the canvas by dragging it in the project window.
4. Save the scene as it has become dirty once you created the prefab.
5. Press play.
6. Press stop and notice that the scene is dirty.

Actual result: Scene becomes dirty.
Expected result: Scene stays not dirty.

Reproducible: 5.5.3p2, 5.6.1p1, 2017.1.0b6
Not reproducible: 5.4.5p1

Fixed: 2017.2.0a1
Reintroduced: 2017.2.0p1