To reproduce:
1) Create new project
2) Add a cube
3) Add Rigidbody and Configurable Joint on that cube
4) Make it a prefab
5) Select the cube in scene
6) Delete Configurable Joint and Rigidbody from it
7) Revert the changes done by clicking 'Revert' at top of Inspector
8) Undo this step with ctrl+z

CRASH

Reproduced in 5.4.0p4, 5.4.1f1, 5.4.2f1, 5.4.4p1, 5.5.0f3, 5.5.0p4, 5.6.0b4
Not reproduced in 5.4.0p3, 5.4.0p1, 5.4.0f3

On 5.4.0f3 this warning comes up when trying to do this:
Component of type Rigidbody was added to Cube using GameObject.AddComponent() and had become dangling during an undo operation.
Use Undo.AddComponent to correctly add a component which can be handle by the undo system