Visible crew/equipment: Just after the meeting Between Hodgins, Angela and the PI, we see a shot of Booth's FBI truck. In this shot you can see the silver camera car reflected in the black paintwork complete with open door for the camera. (00:09:10)
Continuity mistake: When Hodgins holds up the label from the clothes, the way he holds it changes between shots. (00:05:45)
Continuity mistake: At the start, the sweets that Hodgins has got in his hands changes from 1 red lolly to 2 gold coins. (00:04:30)
The Secret in the Soil - S3-E4
Continuity mistake: Just as the gang establish it's a pitchfork Hodgins has an open file in his hands. When the camera changes, he opens the folder. (00:32:10)
The Secret in the Soil - S3-E4
Continuity mistake: When taking her tablets near the start, she has left hand across her lap then up by her head in the next. (00:07:50)
The Secret in the Soil - S3-E4
Continuity mistake: When talking to the victims wife, the daughter givers her some tablets, and she grabs them with her left hand. The camera cuts and now they are in her right hand. (00:07:50)
Other mistake: While driving in the car both Booth and Bones have the windows wide open yet their hair never moves or blows in the wind. (00:14:20)
Continuity mistake: When they get the body back to the lab, both Cam and Bones have their fingers near the forehead wound. When the shot changes, Bones' fingers are now down in the cheek wound. (00:02:30)
Soccer Mom in the Mini-Van - S3-E2
Continuity mistake: Hodgins walks up onto the platform holding a tray of equipment when talking about the victims lawyer. The way he holds the tray and the hand that's holding it, however changes between shots. (00:15:40)
The Widow's Son in the Windshield - S3-E1
Continuity mistake: In the interrogation room Booth shows the girl a picture of her and the victim kissing, and he then clasps his hands together. However, when we see Booth on the screen behind the glass which is a live feed of what's happening inside the room, his hands are clasped.
The Widow's Son in the Windshield - S3-E1
Continuity mistake: When Booth and Cam are talking about hiring Clark, Cam has her hands in a bowl of peanuts in one shot and holding a beer bottle in the next. (00:09:10)
The Widow's Son in the Windshield - S3-E1
Continuity mistake: Just as Booth learns that a cannibal has eaten the victims face, the amount of sandwich he has left changes between shots. (00:05:40)
The Santa in the Slush - S3-E9
Visible crew/equipment: When the santas ask if Chris is dead, a red tape marker is visible on the floor.
Soccer Mom in the Mini-Van - S3-E2
Continuity mistake: At the end sat on the steps of the Lincoln memorial, Bones' arms keep alternating they way they are crossed. (00:42:30)
Soccer Mom in the Mini-Van - S3-E2
Continuity mistake: Max walks into the meeting room with Bones and the guard closes the door. A few moments later the door is closed again. (00:08:25)
Soccer Mom in the Mini-Van - S3-E2
Visible crew/equipment: When the victim goes back to her car at the start, as she grabs the van door a camera man's hand is reflected in the wing mirror. (00:02:05)
The Knight on the Grid - S3-E8
Continuity mistake: When Bones is dragged from the taxi after the explosion, she finds a tooth lodged in her arm (from bomb shrapnel). But she was pulled down for safety by Booth just before it went off, and was not exposed to the shrapnel - she was protected by the car door, and nothing was in a direct line to her. Added to that is the fact that her LEFT arm was hit - the arm that would have been on the 'inside/centre' of the front seat (the bomb went off on the right side of the car), and on which she was most likely lying - completely protecting that part of her body. (00:25:40)
The Pain in the Heart - S3-E15
Character mistake: Zach, from his hospital bed, says he used 3 grams of the monomer to make the explosion. 3 grams of a powder would be a very small amount; less than a teaspoonful. But when he actually did use it, he took a loose amount in a large tablespoon. Zach would have carefully measured it in order to be precise; but he did not. So this is a factual error in what he says; it is also a character mistake in that Zach is the personification of technical accuracy, and would never take a casual spoonful - especially of an explosive.
Suggested correction: Given subsequent revelations, this could be said to be part of everything that goes on.
The Knight on the Grid - S3-E8
Other mistake: The Gorgomon's bank vault discovered earlier in this season, is cluttered with 'stuff'. But in this episode, Zach discovers that multiple mirrors in the area were placed with care (and not randomly) to allow an video/audio device to see 'all parts of the vault'. First-I doubt any camera would be good enough to see much of anything except the one mirror it was looking at, much less multiple mirrored views (Zach used a laser to show the mirror positions). Second-the Jeffersonian staff are examining all the 'stuff' - they'd have to move some things to use equipment, etc. to check them out. It can be assumed they would have put things back in their original place/position, but it would have been impossible to re-place everything in so precisely the same position that the view, via multiple mirrors, would be the same.
Soccer Mom in the Mini-Van - S3-E2
Other mistake: When Hodgins runs up to the platform near the end, to discuss the debris of the watch, the security card reader goes off (as if someone were swiping their card). But there's nobody near it, and we see Hodgins step up the centre of the stairs, nowhere near the machine. About 30 seconds later, Angela comes up as well, but we hear the reader beep, and within a second or so, she's already well up on the platform, much further than possible based on her casual walking speed coming into the scene. (00:37:00)