Reproduction steps:

1. Open "MinimalRepro" Project
2. Open "Main" Scene
3. See that the Scene is marked as Dirty
4. Save the Scene
5. Open the Scene
6. See that the Scene is marked as Dirty

Expected Result: The Scene shouldn't be Dirty because of "Layout Groups" and "Content Size Fitter"
Actual Result: The Scene is dirty on opening it

Reproduced with: 5.6.5p2, 2017.1.3p2, 2017.2.2p1, 2017.3.1p4, 2018.1.0b11, 2018.2.0a4(With a few adjustments)

Note:
Should have been fixed with "966172", but a more specific set-up still reproduces the issue

To reproduce on 2018.2:
Disable the "Content Size Fitter" component on both "GameObject"s
On the deepest child "GameObject", change the "Width" or "Height" to '1.1' (Might need to reload the scene, due to bug 1013029)
On the Canvas objects "Canvas Scaler" component, change "UI Scale Mode" to "Scale With Screen Size"