You seem to be talking about the FBI as a monolithic entity. They are as compartmentalized as any federal entity that might hold sensitive information. It does not matter if there were 1,000 FBI agents a crime scene , it does not matter if fifty took part in accomplishing a crime, only two would need be conscious of what is going on to commit a criminal conspiracy.
How many N.A.Z.I.s were aware of the systematic extermination of Jews (and other groups deemed undesirable) in the early 1940's? We don't know for sure. But not all the Germans were in on it. Remember the Nerumberg trials?
--"I was just following orders...."--
And no, I am not saying a crime was or was not committed at Dent's Run.