Other mistake: Just after Booth realises the drive by was done to help the gang member escape, we see him run up to Bones who's on the forensic platform. However Booth doesn't swipe his pass to allow him entry. Whenever anyone walks up without swiping the card, a siren goes off and the security guard stops them. Regardless of who they are, as demonstrated in several episodes.
Continuity mistake: Booth and Brennan arrive at the crime scene in the beginning of the show. After she has confirmed that the bones in the trunk belonged to a woman, a black car drives by and shots are fired. At first, the trunk of the car is less than halfway opened. Cut to the next shot and the trunk is fully opened.