When attempting to determine the rifle used by the sniper, Stella says it "appears to be a military issued AR-15.". The AR-15 is a civilian rifle, the military has never issued or used it. A CSI would know that fact.
When Mac is interrogating Jerald Brown, he states the Brown had an intelligence level 'Interim Secret' clearance, "that is as smart as they come". "Secret" is a mid-range security clearance level that most military members have or can get. "Interim" indicates that the security clearance investigation isn't complete, but the preliminary findings are acceptable and grants the individual to a limited range of information up to the Secret level. The security clearance has nothing to do with an individual's intelligence.
Just before arresting suspect on airplane at laguardia airport a shot of the airport is shown. A 747 is in that shot. Lag can't handle 747's, runways are too short.