1. What happened
Trying to fix missing script component within a prefab in isolation mode will complain about scripts that are not derived from monobehavior.

2. How we can reproduce it using the example you attached
1. Load the attached project or add the assets to an existing one
2. Select the Cube.prefab asset in the project and open the prefab (Isolation mode)
3. Try to assign script A and B to the missing script component on the prefab
Note that the warning doesn't go away when assigning a script to the slot
4. Try to leave Isolation mode and click on the Save button when prompted

Result: A "Save Failed" dialog will pop up and after clicking the okay button, error will be printed in the console about the scripts we assigned don't derive from MonoBehaviour

Deleting the AsmDef.asmdef asset from the project will make the warning go away and we'll be able to save the changes to the prefab

This is reproducible in all Unity versions since the implementation of Nested Prefab and its Isolation mode. Before, we were simply not able to instanciate a prefab in the scene that has missing scripts in it.