Follow steps to reproduce the issue:
1. Create new project
2. Create a new scene
3. Create an object
4. Attach couple of components to the object
5. Create a prefab of that object
6. Move any component up or down
7. Prefab breaks

vice versa:
Delete the component - no warning message appears that component is broken. case 757828

Reproduced in 5.3.1p2 (9f9ed864cba4), 5.3.1p1 (7d3d8e90548b), 5.4.0b1 (3137382c8e08), 5.2.2p4 (93d0b2db7c56), 5.2.1p4 (9a78a9ce1e6c), 5.1.2p2 (207c2b8718a4)