How to reproduce:
1. Open the attached project ("case_1148404")
2. In hierarchy choose the Cube Gameobject and add the Rigidbody2D component
3. Open the Cube in the Prefab Mode and add the Rigidbody component
4. Exit the Prefab Mode
5. Override the Cube by applying all changes

Expected results: Cube can't have two different Rigidbody components
Actual results: Cube has two different Rigidbody components

Reproduced with: 2018.3.14f1, 2019.1.0f2, 2019.2.0a13

Notes:
- One instance of the same component is removed in some cases (for example, when two same types of Rigidbody are added)
- Improved Prefabs were introduced in 2018.3.0a6
- In the 2018.3.0a6 version Unity crashes, when trying to reproduce the issue