How to reproduce:
1. Open user's attached 'PrefabOverrides.zip' project
2. Open 'SampleScene' in the 'Scenes' folder in the Assets tab
3. Expand Canvas object and go to Prefab Mode by clicking on the '>' symbol on the right side of the 'MainMenu' object's title
4. Go to 'Prefabs folder' in the Assets and rename root 'SimplePanel' and 'TextLabel' prefabs
5. Exit from Prefab Mode by clicking on the '<' symbol. If the issue does not appear repeat 3,4,5 steps some more time

Expected result: Prefab Mode does not cause random creation of duplicates in the Scene
Actual result: Random prefab's duplicates are created in the Scene by closing Prefab Mode

Reproducible: 2018.3.0b7, 2018.3.0b9, 2019.1.0a6, 2019.1.0a9
Not Reproducible: 2018.3.0a6, 2018.3.0b6, 2018.3.0b10, 2019.1.0a5, 2019.1.0a8

Notes:
- The Prefab Mode was added in Unity 2018.3.0a6
- User attached "DuplicationBug.mov" video where the issue is shown