Plot hole: Season 6, episode 8 ("Cloak"). Ziva and Tony enter the secure facility by entering a pass code they obtained by watching the guards enter it previously. Once inside, they open another door using a pass code. How did they know that code? It would make no sense to have both locks use the same code, rendering the second door useless.
Factual error: During the sequence where Bankston and Lee are supposed to make the dead drop of Domino, Adams Tavern, the location of the drop, is shown to be at 2177 Pimmit Drive in Woodbridge Va. The map that is showing the location is geographically correct, but "Pimmit Drive" is actually Horner Road. Also once the action leaves the bar, Lee and Bankston hijack a bus that reads "District Transit Authority". Since they are in Woodbridge, the bus service would be OmniLink.
Continuity mistake: In the scene where Tony and Ziva discover the dead body in Amanda's hiding place the dead body's extended arm is lying on the rug on the floor, and is left that way when Gibbs tell them to leave, yet in the next scene when Ducky shows Gibbs a picture of the dead body, the rug beneath the extended arm has disappeared.
Continuity mistake: During the investigation of the dead wife's crime scene, the arms of the corpse change position from shot to shot throughout the scene, including a moment where the corpse's arms are crossed, then in the next shot Ducky is shown crossing her arms. Ducky is also shown crossing the same arm twice, and the guitar control also changes direction and position with respect to the body.
Character mistake: McGee seeks Director Vance's permission to hack into the Sea Hawk's computer system. He says that in the past four months, he hasn't worked any crime scenes, etc. This is incorrect, as near the start of the episode, he and Ziva go to an officer's home to advise his wife that he is missing. They discover her murdered and then the team, including McGee, are working the crime scene.
Continuity mistake: Episode "Heartland": In the first five minutes of the show, after the guys are beaten up in the alley, when the black guy is laid down on the ground there is a blood stain on the wall, behind where he was standing. When the other guys go to the white guy's aid the blood stain is gone, for about 3-4 shots. When the NCIS team is there gathering evidence the blood is back on the wall.