Booth was shot in the upper right chest during The Wannabe in the Weeds (2008) (3.14), yet in the locker room scene he is shirtless and there's no sign of a scar.
When Agent Perotta is talking to Booth in the interrogation room, it shows the camera behind her and you can see she is writing something but when the camera faces her, she's not writing anything. Then the camera immediately shows her from the back and it's seen she's writing something again but when the camera faces her for a 2nd time, she's not writing anything.
When Hodgins is killing the fish by blending them he takes off the lid but in the next scene he takes the lid off again.
After Booth is hit in the head, Bones states that he should not fall asleep per the doctor's orders. However, medicine is moving away from the idea that people shouldn't sleep following concussions, as sleep can actually be extremely beneficial to recovery as long as the person is monitored for a few hours post injury to check for worsening symptoms.
It's supposed to be deep winter with frozen solid lake ice but in the street scene of the FBI building immediately after the prologue the trees are in full summer leaf.
When Dr. Jack Hodgins is in the suspect's house and mentions that the gold fish went at it like a Peruvian soccer team in the Andes. It was actually a rugby team that had to resort to cannibalism in the Andes.