The Man on the Fairway - S1-E14
Continuity mistake: When Angela walks over to the wood chipper she is drinking from her drink. Camera cuts and she has her arm with her drink in out to the side. (00:25:40)
The Woman in the Garden - S1-E13
Continuity mistake: When the man who put a hit out on Bones is ambushed by Booth, Booth's grip on his face changes instantly. Note the fingers in front/behind his ear. (00:39:30)
The Woman in the Garden - S1-E13
Continuity mistake: When looking for the plant Hodgins, Bones and Booth are in the 4x4 driving down the road. However in the shot of the car approaching the camera it is not Booth driving. (00:07:40)
The Predator in the Pool - S5-E18
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. (00:06:30)
The Man in the Fallout Shelter - S1-E9
Continuity mistake: Bones puts the skull down on the table facing to the left. Camera cuts and the skull is facing to the right. (00:00:45)
Continuity mistake: Angela asks Bones what the rush is. When she does, Bones' ponytail is down her back. Camera changes angle and now it's over her shoulder without moving her head. (00:12:45)
Continuity mistake: When Booth is interviewing The Man in the Wall, he is stood to the side of the door. Camera changes and now he is in the middle of the door. (00:33:50)
Continuity mistake: We see Bones draw a chalk outline on the floor and it is fairly faint. When we next see it, the lines are a lot more refined. (00:30:30)
Audio problem: When Bones wears the dead guy's hand, Bones says a line about not needing mittens for Christmas. However the audio doesn't match her mouth. (00:07:20)
Revealing mistake: When Hodgins is explaining about decomp gasses, you can see in one shot Angela is mouthing his lines. (00:18:10)
The Rocker in the Rinse Cycle - S5-E19
Character mistake: When Booth mentions the 2007 Led Zeppelin concert in London, he comments that they toured that year. That Zeppelin concert was not part of a tour, but just a one-off reunion to honor the memory of late Atlantic Records executive Ahmet Ertegun. (00:40:00)
The Twisted Bones in the Melted Truck - S6-E8
Factual error: The magnesium shop owner shows a forearm tattoo of "Patton's Third Army," which is actually a patch for the Third Armored Division. Third Army was a large A patch.
The Drama in the Queen - S9-E23
Plot hole: The bullet that killed the victim had plastic associated with the wound. This was explained by the fact that the bullet that killed the victim hit a lane divider as it entered the water, but at the end of the episode it was discovered that the bullet was fired from under the water, negating the possibility of it hitting a lane divider at the surface.
The Plain in the Prodigy - S5-E3
Continuity mistake: Near the start, Cam is carrying sunglasses in her hand; suddenly they are on her face. (00:03:20)
The Beaver in the Otter - S4-E24
Character mistake: About half way through the episode, there is a computer screen with "Chemsitry" on it - a spelling error that should not have made it past editing. (00:24:10)
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.
Other mistake: Early in the episode, when the body from the outhouse is in the lab, the gang are all wearing bio-hazard suits. Sweets' suit has an opening along the rear-left section of the facemask - perhaps 3" long, and a half-inch high - making the point of the suit completely useless. (00:05:10)
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)
The Woman in the Garden - S1-E13
Continuity mistake: Booth and Brennan arrive at the crime scene in the beginning of the show. After she has confirmed that the bones in the trunk belonged to a woman, a black car drives by and shots are fired. At first, the trunk of the car is less than halfway opened. Cut to the next shot and the trunk is fully opened. (00:02:10)