Steps to reproduce:
1. Open the attached project "Case_1195496"
2. Open "SampleScene"
3. In the Hierarchy window Expand "Parent" Instance of prefab
4. Select any two child Prefabs, "Cube" and "Cube(1)" will do
5. In the Inspector window Remove the Box collider when two children are selected
6. In the Hierarchy window Select "Parent" Instance of prefab
7. In the Inspector window press "Overrides" and "Apply all"
-- Select the "Cube" and "Cube1" separately and notice that Collider is not removed from one of them, also the "Cube(2)" prefab might have an additional Box collider created

Expected results: Parent Prefab should override everything to Child Prefab GameObject
Actual results: Prefabs are preventing correct overwriting for their parent if the Parent is a Prefab

Reproducible with: 2018.4.0f1, 2018.4.12f1, 2019.2.12f1, 2019.3.0b10, 2020.1.0a12

Notes: This Behaviour is not present when making changes in Parents Prefab edit mode, this only happens in the Sene view.