To reproduce:
1. Open a new project
2. Created a game object in the Hierarchy
3. Make a prefab out of it
4. Select the prefab in the Hierarchy
5. Press apply in the Inspector window
6. Observe as the scene becomes dirty
7. Save the scene and repeat step 5 without making any changes

Expected result: scene does not become dirty since there are no changes made
Actual result: scene becomes dirty, even tho no changes are made

Reproduced on: 5.5.5f1 5.6.4f1 2017.1.0f3 2017.2.0f3 2017.3.0b7 2018.1.0a2