Hi,
You are likely referencing a scene Object from the prefab, and it's something Unity doesn't allow. So when you instanciate that prefab it doesn't have that reference anymore.
You need to plug scene object reference on the fly after you created a prefab instance, either the instance finds what it needs in the scene or you have some sort of manager ( for example the fsm that created that prefab instance), and it inject directly the reference needed to the newly created instance.
Check out the Ecosystem sample "Prefab Instantiation" for a working example, it features some ways as explained above.
Bye,
Jean