At 07:10- The engine order telegraph is set to engines stop yet earlier at 05:25- the Chimera is clearly steaming.
Tony rips off a small piece of the straw wrapper, and blows the rest of it at Ziva. When the camera cuts back to him, he has both pieces of the wrapper in his hands.
As Ziva returns her concert ticket to Abby, Abby's left wristband is missing.
Gibbs grabs the radio to communicate back to the helicopter, as he does, he lifts it in his left hand to his mouth, in the very next shot, the radio is now in his right hand.
The director says she has Top Secret clearance and is told the Chimera's mission goes beyond that. The director of any investigative agency is always cleared for everything, for obvious reasons. No director is ever limited to Top Secret alone.
Skinner reads in Sheppard prior to having her sign the non-disclosure agreement. In reality the NDA must be signed before the details of the program are revealed.
At 05:58- A United States Navy ship would never have unsecured cargo.
Ducky asks Tony to perform a blood count by adding Methylene Blue to a blood drop on a slide. A blood count can never be done this way, and a blood smear stained with Methylene Blue would never look like it does in this scene - rather than a smokey blue color, this slide has been stained with hematoxylin and eosin.
As the director of a government agency Jenny would know that revealing classified material of any kind would be considered a felony, so would not reveal anything concerning the Chimera. Skinner should not have to ask Jenny to sign a non disclosure treaty.
Not only do the "Russians" have strong accents, but the orders "secure the bridge" and "find Ferris" are given in the wrong grammatical form (infinitive rather than imperative).
Ducky refers to the Russians as "Soviet state-sponsored pirates." The Soviet Union ceased to exist in 1992.
At 28:47- Since ships at sea use electrical generators to generate electricity it would be logical for anyone troubleshooting a ship-wide power outage to begin in the generator room.
When the commander is 'reading in' the Director, the cover sheet shown in the briefcase is the standard blue Confidential cover sheet. Confidential is the lowest level of classified US material. The levels are Unclassified (green), Confidential (blue), Secret (red), and Top Secret (orange).
Tony should not blame rats for carrying the pneumonic plague. Rats carry the infected fleas that, upon biting a human, can transfer bubonic (not pneumonic) plague to that person. Pneumonic plague is generally transferred by being in close proximity to an infected individual.
At 31:03- The officer in charge of the secret mission, Commander Skinner, mispronounces the word species as spee shees.