Continuity mistake: Tony boards a helicopter to go to Puerto Rico. When he lands, it's a different one. The first has the number 406 on its side.
Continuity mistake: When DiNozzo rings Gibbs, we can see Kate taking metal scrapings on a pole that has tape on it just above her hands. When we get a closeup of Kate, the tape is not there. (00:25:50)
Continuity mistake: When the lady at the base exchange is throwing stuff at Tony, Tony has a yellow shirt in his hands that disappears, only to be thrown again. (00:24:00)
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