Reproduction steps:

1. Open "MinimalRepro.zip" project
2. Open "Scene1" Scene and see that it's dirty
3. Save the Scene and Re-open it
4. Step 2-3 for "Scene2"

Expected Result: The Scenes shouldn't get dirty just from re/opening the Scene
Actual Result: Opening the Scene marks it as dirty

Reproduced with: 2018.1.0b5, 2018.1.0b1, 2018.1.0a1, 2017.3.1f1, 2017.3.0f1, 2017.3.0b11, 2017.1.3p1, 2017.1.0b3, 2017.1.0b1, 2017.1.0a1, 5.6.5p2, 5.6.0p4, 5.6.0f3, 5.6.0a1, 5.5.6f1, 5.5.3p1, 5.5.0f3
Did not reproduce on: 2018.2.0a2 (24e3a1), 2018.2.0a1, 2018.1.0b9, 2018.1.0b6, 2017.3.1p2, 2017.3.1p1, 2017.3.0b1, 2017.3.0a1, 2017.2.2f1, 2017.2.0f1, 2017.2.0b1, 2017.2.0a1, 5.5.3p2

Note:
Opening this project in any other version than the one it was created with prompts "Timestamps (99) and assets (65) maps out of sync - repairing..." warning
in the console. Deleting "Library" folder before opening this project on another version of Unity eliminates the warning messages.

"Content Size Fitter" needs to constrain at least one "Fit"

If the project is opened in a version where the issue is "Fixed", it doesn't reproduce, untill the prefab is deleted from the scene and added again (Gif attached)

Only reproduces if there is a prefab, set as a child of the object that has the "Layout Group" and "Content Size Fitter" components