Tony says that he worked in the transit department in Baltimore PD for two years. However four episodes later in Stakeout (2008) he reveals that during his time in Baltimore PD he worked in narcotics.
Abby states they used a suppressor due to striations on the slug. Wrong. Bullets do not make contact with any part of the suppressor. To do so is considered a baffle strike and will end badly.
The reflection of the Admiral in the biker's helmet is not reversed; it's an obvious optical effect using earlier footage.
Abby identifies the shell casings at the crime scene as coming from either a GLOCK or Beretta. The striker from the GLOCK and firing pin of the Beretta each leave a distinctly different looking mark on the primer of the shell casing. A forensic scientist (especially one of Abby's ability) would not confuse the two.
Tony DiNozzo chides Ziva David for not assimilating into American culture because she doesn't use contractions in her English. However, in the scene with the vending machines, she does use contractions. (She does in other episodes as well.)