About 10 minutes in, they tip the dead guy over to see where the bullet went. The bunk is covered in blood, yet when a hand retrieves the bullet there's no blood in the bunk. Correction: The shot wasn't of the bullet being retrieved, it was Gibbs picking up the bullet case from the floor.
Dr. Cranston says that McGee has an "Ivy League" education. McGee's degree is from MIT, which is not an Ivy League school.
McGee discovered one of the Navy crew members, who lived in Virginia, had a registered Tokarev pistol. The state of Virginia does not register guns, and does not have any registration database to search.
While in her lab, talking to Gibbs, Abby says that the ammunition used was 25mm which is one inch. The caliber had previously been declared to be .25 which is 1/4 of an inch. Huge difference, and not an error the character would have made.
The bullet was determined to be a Tokarev round, which is 7.62 x 25mm. The 25mm refers to the length of the loaded cartridge, not the caliber.
In S08E14 "A Man Walks Into a Bar..." a boom mic is visible around minute 33 in the center top of the frame.
There is no way for Abby to determine the country of manufacture for the TT33 from the bullet as they were made to the exact same specifications in several Eastern Bloc countries.