I'm not sure what you mean. Unless it's a federal crime, the FBI is usually invited to assist with cases. It's not like they can barge in and take over an investigation. I don't ever even really remember thinking that they didn't have any authority.
Unless you're talking about the conspiracy angle... then that was the whole point.
I think the OP is complaining about it being the same monster-of-the-week format as Kolchak: The Night Stalker. Which Chris Carter always acknowledged as an inspiration