"MissingReferenceException" is thrown on applying changes through override window when a component is removed. Refer the attached video.

Steps to reproduce:
1) Create new project
2) Create empty gameObject > Drag and drop in project to make a prefab "A".
3) In hierarchy, select prefab A > Add Mesh Renderer > Apply.
4) Remove Mesh renderer component
5) In override window > Select Mesh Renderer > Apply to prefab

Actual result: Component does not get removed completely and "MissingReferenceException" is thrown on clicking the compnent.

Expected result: Component gets removed gracefully.

Occurs on: 2019.3.0a7, 2019.2.0b7, 2019.1.0a11

Working fine on: 2019.1.0a9

Note: Unable to test on 2019.1.0a10 due to bug 1102102

Environment: Both Windows and Mac.