Before the flight deck crew strips one of the arresting wires, an S-3 Viking lands, however, when it rolls out and releases the wire from the tailhook it is an E-2 Hawkeye.
When the LSO (Landing Signal Officer) calls "Ready Deck E2, call the ball" the E2 is shown with its landing gear up. The E2 was coming into the break and if this call was made, it would not be done until the landing gear was lowered.
The carrier shown after the course is set to 270 (returning to port after rescue mission) is the Carl Vinson (CVN-70), not the Enterprise (CVN-65).
When the rescue helicopter takes off, it has the number "612" on the fuselage. When it lands, it has "5".
When Tony and Kate attempt to track down the records office, the scene shows clips of the two traveling different paths through the ship. The clips of Kate as she moves through the ship show her wearing a purple turtle neck with her hair in a ponytail. However, when she talks with Tony and arrives at the records office, she is wearing a green zip-up sweater with her hair half pulled back. The clips of her moving through the ship were recycled moments from when she first arrives on the ship and is trying to find her way around the different decks.
The corpsman states that his finger prints are suppose to be on the bag, but any paramedic, medical technician, corpsman, doctor, or nurse ALWAYS wears gloves when working. His fingerprints should NOT be on the bag, even if he was the killer.
The Air Boss (yellow shirt) is wearing an Admiral's CVN65 ball cap instead of a Commander/Captain's. Typically the Air Boss is a senior Commander (occasionally, a junior Captain). In either case scrambled eggs for both the Commander and Captain are the same with less "eggs."
When the "drugged" green shirt comes onto the flight deck, he asks (to nobody in particular) if the E-2 had called the ball, implying he just heard him do that. That comm is not broadcast over loudspeakers on the flight deck.
When the crew are being rescued from the yacht the crew doing the pick up is actually Royal Australian Navy not US Navy. The rank insignia is different as are the helmets. Australian flags are clearly visible on their sleeves and "Australia" on their shoulder boards.
This episode is supposed to take place on The USS Enterprise (CVN 65) but all the shots are from the USS John Stennis (CVN 74) which is a Nimitz Class Carrier. This includes (1) a shot of the PLAT (pilots landing aid camera) when the NICS agents are talking to the Captain on the bridge shows a "74" indicating CVN 74). (2) shot of VAW-112 E-2 on the hangar deck (as the NCIS agents are walking by) which includes "USS JOHN STENNIS" stenciled on the side of the aircraft's fuselage.
When the "drugged" green shirt comes onto the flight deck, the arresting cable is not taut - not in position is would be for an aircraft getting ready to land. If a cable was not "in battery" it would be removed before allowing an aircraft to land.
When Ducky is talking to Wilkes on the autopsy table his eyelid moves.
At the end of DiNozzo's interview with CPO Reyes on the flight deck, Reyes tells DiNozzo, "If there is nothing else, I'd like to prepare for the next aircraft ... sir." However, this was apparently a post-production overdub, as Reyes can clearly be seen delivering a different line than "for the next aircraft".
At around the 24-minute mark when Burley and Gibbs are speaking in the corridor, the visor of the camera can be seen twice. Once when Gibbs turns to confront Burley, and again on the subsequent tracking shot.
Using medical equipment cannot possibly be a common way of cheating a drugs test, unless the corpsman is supplying it.