Scully claims the address of the "Mad Hatter" (Roche) to be 9809 Alice Road, apartment number 6, but when they go to the apartment it is apartment number 5.
Around 00:35:38, we can see marks of the wheels during tracking out on the wet ground.
Fox has already confirmed that Samantha was taken by aliens, so why does he even for a moment entertain the possibility that she was killed by Roche?