Factual error: Air Force One landed in Wichita, Kansas. The local coroner claimed jurisdiction for Wichita County. The city of Wichita, Kansas is in Sedgwick County, in southern Kansas. Wichita County, Kansas is in western Kansas, about 250 miles from the city of Wichita.
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.
Other mistake: Season 5, Episode 12, "Stakeout": The picture on McGee's camera phone is just wrong. It shows not just the man in front of him, but it also shows a hand, holding a camera phone - McGee's camera phone. In other words, the phone is showing a picture of itself and the man, instead of just the man.
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.