How to reproduce:
1. Create a new Unity project
2. In the Project window create a new Prefab
3. Drag and drop the prefab to the Scene view
4. Take a look at the Scene name in the Hierarchy
5. Undo your action (CTRL+Z)
6. Take a look at the Scene name in the Hierarchy

Expected result: After the undo Scene is shown as unmodified
Actual result: After the undo Scene is shown as modified

Reproducible with: 2018.4.9f1, 2018.4.30f1, 2019.4.16f1, 2020.1.17f1, 2020.2.0f1, 2021.1.0a10
Not reproducible with: 2018.4.0f1, 2018.4.8f1

Note:
- Dragging the Prefab to the Hierarchy makes the Scene Dirty and undoing that makes the Scene not Dirty successfully
- Prefab is mentioned for reproduction purposes, the issue occurs with Models, that create a GameObject in the Hierarchy
- If the Scene is modified it is indicated by the " * " at the end of its name in Hierarchy