In the ending scene, Tony asks Pendergast for her number in writing, again. Roughly 10 minutes prior to that when Pendergast is in the parking garage, Tony calls her cell, from his cell.
Nelly Benin's Russian (shown as Russian Federation) passport has the date of issue written as 05.14.2011. Russia, along with most of the world, uses the date format dd.mm.yyyy, so it should be 14.05.2011.
When Gibbs and Pendergast enter autopsy to speak to Ducky you can just catch Abby in the lift waiting for her scene.
It is not explained why the Secretary of the Navy feels it's necessary to hold a secret meeting in the basement, in the men's toilet, of all places. MTAC is where "secret" meetings are usually held -since it's the "secure" room in the building.
The cops in the park don't see all the blood on the lady's back.
A motor powered by a single dry-cell battery could not develop enough torque to behead someone.
The ambulance attendants couldn't be bothered to do the cursory examination of the woman before loading her.
It is never explained -how the little "choke hold" machine gets it's power.
When the team enters the bar, Gibbs spots the scientist and says "McGee, your one o'clock", but her location is more like McGee's 10 o'clock. 12 o'clock is straightforward, 1 o'clock would be slightly off to McGee's right. 10 o'clock is not quite 90 degrees to his left, which is where he looked.
During Ducky's monologue about berserkers, he uncharacteristically mispronounces the Latin name of the fly agaric mushroom (Amanita muscaria) as "Amarita".