The removed component doesn't disappear completely from the Prefab Instance even after Applying changes to Base also MissingReferenceException is thrown while Click Setting Cogwheel of the removed component

Steps to repro:
1. Create a new project
2. Hierarchy > right-click
3. 3D Object > Cube
4. Drag Cube to Project window to create a Prefab
5. Remove Box Collider component from Cube instance
6. Click Setting Cogwheel of the removed component
7. Select "Removed Component > Apply to Prefab" to apply changes to the base Prefab

Actual Result:
The removed component doesn't disappear after selecting "Apply to Prefab"

Expected Result:
Component disappears on selecting "Removed Component > Apply to Prefab"

Occurring with:
2019.1.0a11

Working with:
2019.1.0a9, 2018.3.0b12
Note:
1. 2019.1.0a10 - Unable to repro on 2019.1.0a10 because of this bug - 1102102 "[Win10] Removing prefab instance's component throws an exception in the console and Inspector window is broken"
2. The same issue occurs on applying prefab from an override window
3. Refer attached video for better repro steps.

Environment:
Windows & Mac.

VERIFIED Fixed 2019.1.0a13, 2019.2.0a7