Revealing mistake: The producers have not taken enough generic shots of the places the gang hangs out at; the Royal Diner, & the Founding Fathers. If paying attention (or, watching multiple episodes in a row), one will notice the same people wandering down the street an awful lot! As well, outside the Royal Diner, there's a weird-shaped street corner, that appears to force all traffic in front of the Diner. This would be due to the size of backlot being limited, and certainly doesn't look right.
Revealing mistake: When Hodgins is explaining about decomp gasses, you can see in one shot Angela is mouthing his lines. (00:18:10)
Revealing mistake: In the woods, look carefully and you will see Sherman is holding the cuffs behind his back rather than being actually cuffed. (00:31:30)
Revealing mistake: When the town doctor confirms the clothing of the female victim you can see the victim is breathing despite missing a heart and being dead for a week. (00:33:10)
Revealing mistake: When taking Bones to infested trees, Ranger Rivers stands sideways. In this view, it is shown that he is not wearing the handcuffs on his wrists. Instead, they are just held in his fingertips.
Two Bodies in the Lab - S1-E15
Revealing mistake: Bones rolls backwards to pick up a gun. However, when she stands up she's emptied handed until a few seconds later when she has it taken off her. (00:35:30)
Two Bodies in the Lab - S1-E15
Revealing mistake: At the end, Booth takes a shot at the rogue agent who drops his gun. The only problem is Booth's shot misses the other agent. (00:39:20)
The Skull in the Desert - S1-E17
Revealing mistake: When they find the body of Joesph, you can see him breathing despite him being dead. (00:15:50)
Suggested correction: Joseph is not dead, he's just beat up.
Mother and Child in the Bay - S2-E2
Revealing mistake: When Bones and Booth are driving in his SUV talking about Abraham in the Bible, you can see that Bones' side window is lowered almost all the way down, but her hair is perfectly still and not being blown around as it normally would be.
Revealing mistake: Near the end we see the black FBI vehicle driving over the mine dust and there are tyre marks from previous takes visible. (00:34:20)
Revealing mistake: When Booth is running down the hill, there are marks in front of him from previous takes. (00:36:00)
The Glowing Bones in the Old Stone House - S2-E20
Revealing mistake: When Booth does the U-Turn after working out who the killer is, In the clip of the SUV turning you can see skid marks on the road from previous takes. (00:37:00)
The Verdict in the Story - S3-E13
Revealing mistake: At the end where Brennan is waiting outside the courthouse, you can see Booth's (David's) arm. You can see it just to the left of the large column on the right side of the screen. It is there before he leaves the courtroom, and before he walks up. He is supposed to be walking to her from the courtroom, but the actor is instead waiting behind the pillar for his cue.
Revealing mistake: After speaking to the children the victim used to look after, the scenery outside the car shows the car is going forward when we see Booth but when the camera is on Bones, the background is going backwards. (00:17:50)
Double Trouble in the Panhandle - S4-E12
Revealing mistake: At the end, the stunt double for Bones is visible when she falls off the high wire. (00:39:15)
The Proof in the Pudding - S5-E12
Revealing mistake: Hodgins says that the two shots took 1.6 seconds exactly. However, the timer shows a time of 1.15 seconds. (00:29:00)
The Gunk in the Garage - S8-E3
Revealing mistake: Dr. Sweets gets shot by a stray bullet. However, before they fire their guns when Dr. Sweets says "they have guns" he already has the blood shot stain on his shirt. (00:39:10)
The Spark in the Park - S9-E11
Revealing mistake: When the burning leg lands on the witness at the start, the flames are super imposed. (00:01:55)
The Fight in the Fixer - S11-E15
Revealing mistake: Hodgins turns the furnace off at the start. However the yellow light from the flames in the tunnels disappears before he turns the furnace off.
The Final Chapter: The Flaw in the Saw - S12-E6
Revealing mistake: At the very end we see Bones and Booth on the rolling log. In the front view the log is obscured from shot however it's clear from the motions of Booth and particularly Bones that they are stood on level ground, mimicking the actions of being on the log. (00:41:00)