When Tony goes onto the flight deck we can see an F-18 parked near the end of the flight deck. When we see the ship from behind the plane has become an F-14. The F-14 was retired from US Navy service in 2006 and would not have been on board an operational aircraft carrier.
When McGee is taking photos of the crime scene, he accidentally shoots camera flash into Ducky's face. In the photo we can see Ducky carrying scissors in the pocket on his chest, but when the screen switches to 'real-time' view of Ducky, the scissors are missing.
At the end of Season 5 Judgment Day (Part II) (2008), Vance assigns DiNozzo to be Agent Afloat aboard the USS Reagan but when Season 6 began DiNozzo is the Agent Afloat aboard the fictitious aircraft carrier USS Seahawk.
When the Medivac COD is turning on the flight deck prior to take off it has a number 22 on completion of the turn it is number 25.
Satellite phones would not work below deck on a ship as Gibbs was shown doing in Agent Afloat (2008).
The USS Seahawk has the hull number CVN-65 (carrier vessel nuclear), as seen on the caps that some of the crew wear. There is no actual aircraft carrier called the USS Seahawk; this is actually the hull number for the USS Enterprise. The exterior shots of the ship are, however, clearly not the Enterprise but a newer, Nimitz-class carrier. In the first establishing shot in this episode, the hull number painted on the deck of the carrier is 74, corresponding to the Nimitz-class USS John C. Stennis.
When Gibbs is in the coroners office, DiNozzo say the report say's "blunt force trauma resulting in the nasal bone penetrating the brain. This can not since the nose bones are much more brittle and would crush and most of the nose is cartilage. And just the site of the corpse shows the nose completely intact.
The Agent Afloat was called to the fantail over the 1MC. DiNozzo ran to the aft end of the flight deck. The fantail is several decks below the flight deck.
In the opening scene, when Ziva looks in the window and sees the corpse, the corpse is visibly breathing.
When Tony finds lieutenant Evans, he checks his dog tags and confirms that it's Evans. If the man impersonating Evans on the Seahawk wanted to maintain his cover he would have taken the dog tags as well as the ID card.
When Gibbs is speaking with Seahawk's Captain, the Captain says, "I'll increase security on our weapons systems and the reactor..." The two ships used to stand in as Seahawk each have multiple reactors. USS Enterprise (CVN-65) has 8, USS John C. Stennis (CVN 74) has 2.