Though it is painted to look like a Washington D.C. bus the motor coach that Gibbs chases Agent Lee and the suspect onto is actually a San Francisco MUNI coach with the line number '4 Sutter' and a destination of '30th St'.
At 05:17- There just happens to be satellite imagery of two people out in the middle of the forest; one of them being Lee's kidnapped daughter.
At 03:35- Tony doesn't sidestep Lee and continue to follow the suspect.
Tony quotes Cary Grant as saying "Judy, Judy, Judy" in North by Northwest (1959). Grant not only does not say that in this film, he doesn't say it in any film.
When DiNozzo and Ziva are talking about team members' secrets, DiNozzo mentions that he knows where she has a small tattoo. Jews, especially Israelis, do not tattoo their bodies because Hitler had Jews' arms tattooed with ID numbers during his reign.
Tony and Ziva don't think to just put an insulator in between the contacts on the girl's bed. The blanket Ziva removes from the bed would have done the job.