I am not a retired FBI person, but the answer to your question is compartmentalization. If you run a series of investigations out of the top floor of the FBI (highest levels) it is unlikely 99% of agents know anything about it.
Information goes up the chain and they don’t push information about “national security investigations” or “counter-intelligence” down the chain to field offices or field agents.
John Solomon and Dan Bongino have both explained this well. Everything they did against Trump or to protect Hillary was done under the disguise of national security so it was “need to know” and heavily compartmentalized so only a handful of people knew some of the story and only a few knew all of the story. We saw this with some of the officials during the hearings where they (remember Page’s reaction?) were surprised to learn important information.
That field agents would be assigned only one segment of a investigation and then turn it in.
Still difficult to imagine that all agents could be kept in the dark on major political spying investigations.