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: 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: We see Ziva take the photos out and place them on the interrogation table and ask the captain to point out their suspect. We then see the Captain pick up a photo. Camera changes to McGee and Tony behind the glass and we see Ziva getting the photos out and places them on the table again.
Revealing mistake: When the Lieutenant is explaining how her gun was in the victim's house, the camera pans behind Gibbs. Pay close attention and you can see a very faint shadow move across his back. Since we see there is nothing behind him on numerous occasions, it can only be part of the film crew.