How to reproduce:
1. Open the user's attached "PrefabBug.zip" project
2. Open the "SampleScene" Scene
3. Create an empty GameObject in the Hierarchy window
4. Select the newly created GameObject
5. Add the "ScriptWithPrefabRef.cs" script to the GameObject
6. Drag the GameObject from the Hierarchy window to the Project window to create a Prefab
7. Select the GameObject in the Hierarchy window
8. Press ">" in the Hierarchy window to go to the Prefab editing window
9. Drag the created Prefab into the "Test Prefab" field in the Inspector
10. Exit the Prefab editing window
11. Select the referenced object in the "Test Prefab" field in the Inspector

Expected result: The Prefab gets referenced in the "Test Prefab" field
Actual result: The Prefab's instance in the Scene gets referenced in the "Test Prefab" field instead of the original Prefab

Reproducible with: 2018.4.26f1, 2019.4.8f1, 2020.1.3f1, 2020.2.0a21

Note:
- In the user's project, SerializeReference attribute is used on the "Test Prefab" field, but it also reproducible without any attributes