When Tony, Ziva, and McGee set off to check out Kirby's apartment, McGee's hair is considerable shorter while in the parking lot than it was when he left the squad room.
During an interview with Kirby (or Smith, depending on the place in the story - about 53 minutes in) Wilson Bethel's (the actor playing the character) hair keeps switching. From scene to scene it goes from being parted on his right side to his left side and back again.
A 9mm is stated as a low speed round, when in fact it is a high speed round that has a tendency to go through things. This was one of the reasons for a widespread switch to .40 caliber weapons which is less likely to go through people and buildings.
At one point in the dialogue Tony refers to the victim as "Seaman Smith", whereas he's not a seaman (E-3) but rather a petty officer and a storekeeper second-class (E-5).
Towards the beginning, when Ducky and Palmer are talking at the car crash crime scene, after Ducky tells Palmer he hopes he brought more suitable shoes, then says he has a driver's license but wouldn't turn up at the Indy 500 with his Morgan, his mouth continues to move, it's obvious it was dubbed over.
The team seems to go back and forth to Norfolk in a matter of minutes which isn't possible. Norfolk is at least a 3 hour drive from DC.