The best example of this I can think of is the "100 mile from the border Constitution-free zone", which was the stated position of some moron at DHS that was then (maddeningly, given how great they normally are) picked up by the ACLU. In reality, the notion that there's a 100 mile zone of warrantless personal searches extending inward from every border was a notion that was litigated by SCOTUS in the '70s and, obviously, found wanting.
I would support a public policy that would make statements of this sort ("the CIA has no limits when working with the NYPD!", "We can ghost your laptop as long as you're within 100 miles of any airport!") a firing offense, but short of that, there's not a lot you can do about this problem; if the USG employed 1/4th the number of people it does now, that'd still be over a million people, and no group of one million people can possibly avoid a couple crazy people.
The real check on this sort of stupidity is the courts.