The statement that Brennan makes that the impression in the gum was as good as a fingerprint is completely false. It never been proven that human dentition is unique to an individual, it is also subject to change with every restoration, extraction or orthodontics by a dentist, fingerprints are not subject to change. The National Academy of Sciences itself has stated that "The uniqueness of the human dentition has not been scientifically established".
You cannot match a tooth impression to dental records. Dental records consist of x-rays and patient notes, not 3D molds.
In the opening sequence with the paint ballers, about half of the characters are using paintball guns without the paint ball feeders at the top or the pressurized air tanks at the back.
When Booth is taking a picture of the body Bones is crying over, his phone shows the logo of the FBI, rather than what he was taking a picture of.
Cam asks Hodges, "So they dug up a bag before burying him [the victim]?" However, the victim was female, and Cam already knew that.