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?"
Visible crew/equipment: As Gibbs, Ziva and Tony enter the Nelson home with guns drawn; just after Ziva enters, a man can be seen reflected in the door's window (Gibbs and Tony are in frame, and there is no other character there). Tony enters, then Gibbs - and we see the cameraman reflected also. (00:19:45)
Other mistake: When McGee tells Gibbs that Nelson erased his entire hard drive, the camera shows the diagnostic he is running - "Primary Drive Erased: 100%." Yet the details below show 93GB used of 111GB total, and the drive letter is G: (not C: as it would most likely be.) It could be argued that his C: drive is simply an OS drive, and G: is his data drive, but still, 93GB used is not 'erased'. (00:22:05)
Revealing mistake: Part 1 - As Tony eats his donut, and spills the jelly on his shirt, it's clear that (the actor) is moving his body to make that 'accident' happen as scripted. As the jelly begins to leak out, he doesn't move; because it doesn't fall as expected, he jerks suddenly, to make the jelly fall on his shirt. He stops moving, 'shocked' at this, holding the donut with both hands. Part 2 - The camera angle changes to 'behind' him, and he is only holding the donut with one hand. Part 3 - He then grabs at a napkin (just out of frame) to clean it off; the camera cuts to Ziva briefly, then back to Tony, who does not have any napkin. (00:24:55)