Plot hole: We see Gibbs fire his sniper rifle and kill Saleem from a hill several hundred meters away over hilly and sandy terrain. We then see him shoot a guard while Tony and McGee are getting free. By the time they have walked down the corridor (about a minute) Gibbs has appeared in the hallway in full desert sniper suit. (00:40:00)
Plot hole: For such a dangerous serial killer, Lt. Cobb should be more securely restrained than he is. He wears a simple pair of handcuffs, with only one security escort.
Lt. Jane Doe - S2-E4
Plot hole: It really doesn't make sense that they found the real killer from Jane Doe #1 assuming he also killed Jane Doe #2. They only found him because they assumed he was in prison for the last 10 years. One could explain that he must have gone to prison shortly after the first murder because he said he'd be back but wasn't, but that he was actually recently released is just pure coincidence. And without finding him they would never have suspected Officer Cluxton.
Plot hole: Season 6, episode 8 ("Cloak"). When Ziva and Tony take the elevator two floors down this takes a full minute. When in a hurry for a call it speeds down, yet for this conversation it (conveniently) took a minute.
