In the Cafe, Lee places a lipstick mark on the coffee cup lid. It aligns with a line of check boxes. Later, the lipstick is aligned off to the left of the boxes.
Tony quotes Cary Grant as saying "Judy, Judy, Judy" in North by Northwest (1959). Grant not only does not say that in this film (nor is there a Judy), he doesn't say it in any film. He might be confusing it with Only Angels Have Wings (1939) where his love interest is Judy MacPherson, played by Rita Hayworth, he has a line that goes "Hello, Judy. Come on, Judy. Now, Judy." but he never says "Judy, Judy, Judy".
The hair being sent by the kidnapper as proof of life has smooth edges on one end, indicating it had been cut off. Which would make it impossible to get a DNA sample; only hair that still has the follicle attached, either from being pulled out or shed, would have enough DNA for a usable sample.
Abby says the kidnapper must have had his identity erased because his fingerprints aren't in the system and didn't match to any banking history or credit history. However it is not unusual for a person's fingerprints to not be in the AFIS database, fingerprints are not needed for opening most types of bank accounts or loans. For the kinds of federal loans that require a federal background check, which is a small minority, a person's prints are only stored at that local bank's branch office and ran against the criminal database, they are not stored in AFIS. Same thing for those who are fingerprinted when buying a gun, their prints are ran against the AFIS criminal database but not uploaded to it, only the FFL dealer the gun was purchased from keeps the prints on record, and they aren't stored electronically. Besides those arrested and charged with a crime only people who served in the armed forces, federal government or state government employees, law enforcement personnel and employees of government contractors have their fingerprints saved in AFIS.
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'.
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.
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.