Character mistake: When Bones and Dr Hodgins, who is proclaimed as a seasoned diver in a previous episode, are in the tank, Bones gives an instruction and Hodgins replies with a thumbs up. Since Bones is diving as well, they both would know from certification (without which neither would be allowed to dive in the facility) classes that a thumbs up is the hand signal for "I'm ascending", not OK or any form of acknowledgement. They either are not certified divers or they should have immediately surfaced.
Continuity mistake: When Brennan and Hodgins are in the aquarium tank recovering the skull, the hose for Brennan's air starts over her left shoulder. During the first close up where Brennan is actually retrieving the skull, the breathing apparatus has been reversed, so the hose is now over her right shoulder. All other shots the hose is over the left shoulder.