You cant reference scene objects in Prefabs. This is a standard Unity rule... The Project Hierarchy is like a library while the Scene is like the park down the street. You can go get a book from the library and take it to the park, but the books in the library have no idea whats going on until they are put in the park. There is information about this both here and on the Unity forums.
Typically you use good practices to store relevant variables at the proper time to make it easy to communicate to/from them. For instance using Create Object and storing the result for later use, or Find Game Object, Collision Events, Trigger Events, Tag filtering, etc etc....