When Harvey asks Mike if he knows how we won WWII, Mike jokingly says "Yeah, of course. Spock didn't let Kirk save Joan Collins from getting hit by that car." He's talking about the famous episode from The City on the Edge of Forever (1967), but it was Kirk who stopped McCoy.
The exterior shots of the jet Scotty and Harvey fly in is a Learjet 35. The internal cabin height is 4ft 11in at its highest point, Harvey is 6ft. The set does not match the dimensions of the actual aircraft. The dimensions of the interior set would match up to a Boeing Business Jet or Airbus ACJ.
Rachel states that one of the cases is in Massapequa. Massapequa is not near Boston or Harvard, but is actually in Nassau county on Long Island in New York.