How to reproduce:
1. Connect an external data storage device to your computer (USB flash drive, hard drive)
2. Save the attached project (case-1242265-.zip) in the external data storage and open it
3. Open Prefab 'Cube' In-context Prefab Mode (click the '>' button to the right of the 'Cube' GameObject in the Hierarchy window)
4. Make sure Cube is expanded and Cube (1) and Cube (2) are displayed
5. Select Cube (2) and delete it with a keyboard command
6. As quickly as possible select Cube (1) and delete it as well
7. Make sure Cube (1) and Cube (2) got deleted
8. Go back to the SampleScene Hierarchy

Expected result: Cube and Cube (1) have no child GameObjects
Actual result: Cube and Cube (1) have child GameObjects even though the Cube Prefab does not

Reproducible with: 2020.1.0a5, 2020.1.0b9, 2020.2.0a11
Not reproducible with: 2018.4.23f1, 2019.3.14f1, 2020.1.0a3

Notes:
1 This issue started with the introduction of a new Prefab workflow feature "Prefab Mode in Context". This issue doesn't occur in Prefab Isolation Mode
2. When the issue occurs the Prefab in the Project window displays that it's made of 2 Cubes even though it's made of only 1
3. The issue is not 100% reproducible as the 6th step has to be done quickly