Agent Afloat - S6-E2
Continuity mistake: Near the end, several of the items on Ziva's desk change orientation from one shot to the next.
Murder 2.0 - S6-E6
Continuity mistake: When NCIS catches the killer, the way he holds a dead man's switch changes. In some shots, he holds it with all five fingers, and in others he holds it with his middle two fingers and thumb, with his index and pinkie fingers extended. (00:39:45)
Nine Lives - S6-E5
Continuity mistake: When Fornell walks past the reporters at the court house he passes The Wall. Camera cuts and he has jumped back and isn't near The Wall. (00:36:30)
Deliverance - S6-E15
Factual error: It is constantly mentioned that the number found at the crime scene is Gibbs' military service number. The Marine Corps stopped using service numbers on Jan. 1, 1972 and since has only used Social Security numbers for identification.
Continuity mistake: When Vance shows Gibbs the access card belonging to their dead petty officer, the position of his hand on the card changes between shots. (00:38:35)
Continuity mistake: 6.17 - South by Southwest. The first time Tony is talking on the phone to London about his uncle's estate, he is alternately either talking on his cellphone or office phone throughout the conversation. (00:06:15)
Agent Afloat - S6-E2
Character mistake: McGee seeks Director Vance's permission to hack into the Sea Hawk's computer system. He says that in the past four months, he hasn't worked any crime scenes, etc. This is incorrect, as near the start of the episode, he and Ziva go to an officer's home to advise his wife that he is missing. They discover her murdered and then the team, including McGee, are working the crime scene.
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.
Continuity mistake: Episode "Heartland": In the first five minutes of the show, after the guys are beaten up in the alley, when the black guy is laid down on the ground there is a blood stain on The Wall, behind where he was standing. When the other guys go to the white guy's aid the blood stain is gone, for about 3-4 shots. When the NCIS team is there gathering evidence the blood is back on The Wall.