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. (00:40:25)
Factual error: There is a big deal made about Gibbs giving Shepard one of his magazines in the study with La Granoille. It is implied that that magazine was used in the gun to kill La Granoille on his yacht. The magazine he gave her was for his department issued Sig Sauer P228, however, he was killed with a Glock 19. The magazines are not compatible.
Continuity mistake: When Tony enters the NCIS interrogation room with Fornell, he sits down and places his bag of potato chips on the table. In the next shot, the bag has disappeared, he removes it from his jacket pocket, and places it on the table again. (00:25:15)
Continuity mistake: When Gibbs is trying to talk Lt. Arnett out of jumping off the ledge, Gibbs is relatively close to Arnett in the middle of The Wall when Ducky and Abby watch the live news report, but in real time, Gibbs is over at the far left corner of The Wall. (00:04:10 - 00:05:00)
Continuity mistake: After Ducky finds the needle in the MRI machine it cuts to Gibbs stepping on the bubble wrap, and as Abby happily rolls toward Gibbs, in the two shots facing her the headband magnifiers are flipped down over Abby's eyes, but in the shot facing Gibbs the magnifiers are flipped up over Abby's head. (00:27:30)
Continuity mistake: During season 4 when Ziva gets worried about Tony being 'sick', she is researching y. Pestis, and telling Gibbs how worried she is about Tony having tests and the long-term effects of plague. In season 5, first episode, when Ducky comes to tell the group that the body is not Tony because "he didn't have plague", Ziva looks confused and says "before my time?"