Special Agent Cortez says that she checked the VIN on the boat to find the owner, however boats do not have VINs. Boats have HINs (Hull Identification Numbers).
Shada Shakarki's flight itinerary showed she flew into Dulles (DUL); the airport code for Dulles is IAD.
The hull shape of the boat "Kelly" shown when the vessel is upright is inconsistent with the hull shape the whole time Gibbs is building it, and also when the vessel is upside down being cut up by Abby. The hull shown incorrectly in this episode is a hard chine - it has a strong angle between the side and underneath of the hull; the hull shown as the boat is being built (and also being cut up) is smooth curve - there is no distinct "edge" between the side and underneath, it curves from one to the other.
When McGee explains Little Orphan Annie to Ziva, he says she has "curly red hair, no eyeballs". Little Orphan Annie did have eyeballs, what she didn't have were pupils drawn in her eyeballs.