Continuity mistake: In the episode "Untouchable" (Season 3, episode 20), the camera pans across a line of several anime plushies. When the shot then goes wide, several of the plushies have either been re-arranged or removed completely, including a pink plush and the Kyogre plush. It also seems as though there are two Miroku plushies in the scene as well, one near the middle and one off to the side of the left pillow.
Continuity mistake: When Gibbs and the team meet the sheriff and ask to be shown the crime scene, he states that it was in the Edenvale motel room 8. In the opening scene the door that the gentleman knocked on and subsequently got his feet covered in blood from the body bleeding out was room 1.
Continuity mistake: While Tony and Ziva are outside Ziva's hotel eating pizza, Ziva is eating the pizza in one shot with the slice in the shot, in the shot directly before this and directly after, the pizza is no where to be found and she is no longer chewing.
Continuity mistake: Agent Todd is standing there coat open, hands in her pockets on Air Force One watching Gibbs walk away when the bad guy who is a reporter (Leonard) comes up to her and comments "Loosening your dress code Kate". Seconds later when she turns to indicate that he should return to the press section her coat is now buttoned up.