How to reproduce:
1. Open the attached project "1195283.zip"
2. Create an instance of the "test" Prefab in a scene
3. Notice that the scene is marked as dirty
4. Save the scene

Expected result: Scene is no longer marked as dirty
Actual result: Scene is still marked as dirty

Reproducible with: 2018.3.0a11, 2018.3.14f1, 2018.4.13f1, 2019.2.13f1, 2019.3.0b12, 2020.1.0a14
Not reproducible with: 2017.4.35f1, 2018.3.0a10

Notes:
The issue is reproducible with any Layout Group component added to the parent GameObject.
The issue is reproducible with Image, Raw Image or Text component attached to the child GameObject.
The issue does not reproduce when creating an instance of a Prefab created in an unaffected Unity version.