In the opening crime scene, when the NCIS crew arrive. They walk past the two police vehicles with bullet holes in the windshields. The bullet holes are practically identical as to amount and placement.
The team worry about getting caught using the wire tap on the mayor's phone to catch Bancroft. Why not just fake a call to their office by one of them (say from a public phone box, from where there are no security cameras etc) and say it's an anonymous phone tip? This would be impossible to trace and the wiretap on the mayor would remain in place.