Visible crew/equipment: When Agent Fornell follows Gibbs for a private chat (in the elevator) there's an overhead long shot of Caitlin, Tony, and Fornell's two agents. It then cuts to a shot facing Caitlin, and we can see the white mat taped to the floor with black tape (which was not in the previous shot), at the bottom of the screen. (00:22:50)
Bikini Wax - S2-E18
Visible crew/equipment: When Gibbs joins Caitlin on the beach just as she finishes up her call, in the wide shots their two reddish T-marks (plastic type) are visible on the sand, where each of them stand. (00:06:20)
Visible crew/equipment: After Caitlin shrieks and tells Abby that Gibbs is driving, Abby replies that she's saying a prayer in many languages. It then cuts to a shot of the car Tony's driving, and the reflection of the camera comes into view on Tony's window as the filming vehicle pulls alongside. It's visible again in a following shot. (00:37:40)
Forced Entry - S2-E9
Visible crew/equipment: Right after the intro at the start, when Gibbs and Caitlin get out of the vehicle the reflection of the large reflector screen is visible on the door's window. (00:01:40)
Visible crew/equipment: After Gibbs explains to Agent Reyes that Commander Shields in on Terminal Leave, and she has a four day deadline to solve the case, when Gibbs walks away there's an overhead shot and multiple chalk T-marks are visible on the ground. (00:05:00)
Lt. Jane Doe - S2-E4
Visible crew/equipment: While Gibbs is interrogating Cluxton they are alone in the room, and when he shows her Harlan Wilson's death certificate, in the overhead shot as she begins to snap, the leg of a crew member is visible on the right side of the screen. (00:42:05)
Visible crew/equipment: When Tony open the van's back door to show Abe's "daughter" the weapons they are alone, with Gibbs taking their photos from across the road. There's a closeup of the case of LAWs, and in the next shot a crew member (looking at the actors) is visible at the left side of the screen, standing directly behind them (she's in this shot only). (00:16:10)
Visible crew/equipment: When Caitlin refers to Gibbs as a Gloomy Gus it then cuts to Tony with Abby, and in the following shot facing the glass doors, the reflection of the camera and its operator are visible as they move toward the left of the screen. (00:14:05)
Visible crew/equipment: When Ziva is with Jason Edom in the interrogation room, Ziva sits down and asks him if he's afraid of germs. Then after Edom's closeup, the red T-mark is visible on the floor near the door in the wide shot. (00:31:55)
Visible crew/equipment: During the scenes in Lafferty's house, crew/camera movements are reflected on the large glass fish tank near the front door. (00:27:40 - 00:35:00)
Visible crew/equipment: When Gibbs tells Tony and Ziva to go to Wilkerson's home they pass Abby on their way to the elevator, and just as Ziva waves her hand at Abby, in this shot and a following shot a crew member is visible as he's ducking down by Tony's cubicle, under the monitor on the right side of the screen. (00:04:10)
Visible crew/equipment: While Palmer and Ducky are with the deceased in Autopsy, just as Jimmy mentions that Keller only dated models and A-list celebrities, the reflections of the camera operator and camera are visible on the steel door. (00:26:40)
Visible crew/equipment: While Tony and Ziva are speaking with Tom Crawley about Taylor, the red and green tape marks are visible on the floor in overhead shots, such as when Crawley stands up. Also, near the end, while Gibbs, Ziva, and Tony are with Crawley and the models, more tape marks are visible again. (00:19:20)
Visible crew/equipment: After Gibbs threatens to take McGee's badge if he ever hesitates again, when it cuts to McGee at the lab with Abby, the chalk T-mark is visible on the floor at McGee's feet. (00:42:20)
Visible crew/equipment: While Gibbs flips the pages of the court records from Stewart's case, when he sees the photos he rushes off to the lab, and in the wide shot two green T-marks are visible on the floor, in front of his desk. (00:42:50)
Visible crew/equipment: When Gibbs brings the pizza to Tony at the jail, in the wide shot just as Tony walks over to Gibbs, a crew member wearing white shorts is visible behind Gibbs, on the right side of the screen (where another camera is located). (00:22:55)
Visible crew/equipment: After Abby demonstrates the magic shop knife to Gibbs, when it cuts to Tony surprising the suspect, the T-mark taped to the ground is visible behind the car in this shot and a following shot. (00:40:15)
Visible crew/equipment: After Ziva discovers the hair dye in the hotel room it cuts to McGee with Abby, and as they walk away from the desk, the reflections of crew members, including the dolly grip pulling the camera dolly, are visible on the glass door. (00:39:40)
Silver War - S3-E4
Visible crew/equipment: At the re-enactment field, after Ziva pulls a gun on the two men in the graveyard, it then cuts to McGee and Tony with Kearns while Gibbs is on his cell. Two shots later, the camera becomes visible on the right side of the screen, just as Gibbs walks past it. (00:40:45)
Mind Games - S3-E3
Visible crew/equipment: While Gibbs and Tony are in the car chasing after Briggs, Gibbs is on his cell with McGee getting location updates, and just as Gibbs asks, "How far ahead is he?" the camera is visible behind Gibbs and Tony, by the back seat. (00:37:55)
Answer: I hadn't seen the backdoor pilots yet but while it wasn't explicitly stated, at least onscreen, I heard somewhere Vivian got either fired from NCIS due to jeopardizing a case, got resigned from the agency, or transferred to the FBI.
Raykvega423