The Blackout in the Blizzard - S6-E16
Continuity mistake: Toward the end in the elevator, Bones says there may be a way out by jumping on the seats to break them because of the rusted bolts between the 1st and 2nd seats, and they break. But at the end in Booth's apartment they are sitting in the seats, and they are numbered 1-4, but the seats look like they broke between seats 1 and 2. When the seats are intact there are 5 of them, so it should have been seats 2-5 that were intact at the end.
The Feet on the Beach - S6-E17
Plot hole: Dr. Filmore stated that he was reading on Thursday May 9th and his arm stopped working. May 9th hasn't been on a Thursday since 2002. Hard to believe that he would be working for almost 10 years with his arms being paralyzed.
The Prince in the Plastic - S7-E3
Other mistake: Brennan finds Angela assembling a child's toy. She asks "what is all this?" and Angela replies "this is a walking toy for my girl." But Angela didn't have a baby girl, she had a baby boy - Michael Staccato Vincent Hodgins. (00:15:00)
The Future in the Past - S8-E1
Visible crew/equipment: When Bones is on the platform and everyone has gone from the lab, Sweets arrives and we can see a woman walking behind him. There isn't supposed to be anyone at the Jeffersonian except them.
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 Method in the Madness - S8-E5
Continuity mistake: At the start, Bones is putting her one glove on. Camera changes and both gloves are now on. (00:03:15)
The Method in the Madness - S8-E5
Continuity mistake: When Bones starts to explain about the Aztecs, Hodgins is holding a boot upright. Camera changes and the boot is now upside down. (00:06:40)
The Method in the Madness - S8-E5
Continuity mistake: When Sweets is staying at Booth's and Brennan's house, he comes downstairs after taking a bath and, as he turns, his shoulders are shown without the scars he has in another episode.
Continuity mistake: When Bones scans the pod you can see the skull in the pod has its jaw open. However the skull picture on the scanner has its jaw closed.
Continuity mistake: When Hodgins carries the first box of roaches to the remains, the positions of the roaches changes instantly. In one shot they are all over the side of the tank, in the next shot they are not. (00:21:30)
The Ghost in the Machine - S8-E9
Other mistake: Bones states she doesn't like to make assumptions in sex based on just the skull. However this is something she has done from the start. (00:01:10)
The Corpse on the Canopy - S8-E12
Audio problem: Early in the episode Angela is holding Michael Vincent and you can still hear him crying, but the baby isn't crying. (00:02:00)
The Twist in the Plot - S8-E13
Continuity mistake: When Bones is watching Booth make his video for Christine, in some shots she's stood up straight, in others she's leaning against the wall. (00:38:00)
Plot hole: Angela comes into the autopsy room to inform Hodgins and Cam that Brennan is awake. Cam says that Brennan said the entry wound was cold and Hodgins comes up with the ice bullet theory. But how did Cam know what Brennan said about the cold if she didn't already know Brennan was awake?
The Maiden in the Mushrooms - S8-E21
Continuity mistake: When the guy finds the skull his grip changes between shots. (00:02:10)
The Party in the Pants - S8-E22
Continuity mistake: The body falls on a foreman who gets covered in blood. When she scrambles away the blood has gone. (00:03:05)
The Party in the Pants - S8-E22
Other mistake: The body falls from the excavator revealing there is no other debris in the excavator. However when the team get there they are told that the load in the bucket fell on the body, crushing the head. (00:03:15)
The Party in the Pants - S8-E22
Continuity mistake: When Sweets is talking to the victim's girlfriend, she has a strand of hair in her hand from the rear angle and nothing in her hand in the front angle. (00:15:50)
The Party in the Pants - S8-E22
Continuity mistake: At the reception for Seeley's mother's wedding during the bouquet toss, when the bouquet is in the air the stems are bound in white ribbon, when Dr. Brennan catches the bouquet the stems are loose.