Bones
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The Man in the SUV - S1-E2

Continuity mistake: At the end after shooting Farheed, we see Booth with both hands on the railing. Camera shows a secret service operative opening the camera bag containing the bomb then cuts back to Booth who suddenly has his gun back in his hands and raised as if he had just fired. (00:38:50)

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Pilot - S1-E1

Continuity mistake: When the director is looking at the 2 photos Booth hands him, there is a shot of the two photos one on top of the other neatly. Camera changes and they are no longer neatly on top of each other. The bottom one is sticking out and should have been visible in the previous shot. (00:18:40)

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Pilot - S1-E1

Continuity mistake: Booth hands over a couple of photo's to the director about the case they are working on. The director is holding the photos at the bottom in one shot and the top in the next. (00:18:40)

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Pilot - S1-E1

Continuity mistake: Just after Bones has put the skull back together, we see Zac put down a drink and put his hands in his pockets. Camera cuts and one hand is back on the table. (00:12:20)

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Pilot - S1-E1

Continuity mistake: Bones asks Zack for water samples and a few other things. When she does we see he has his camera in his left hand. Camera changes and now his camera is in his right hand with no time to swap hands. (00:05:10)

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Pilot - S1-E1

Continuity mistake: At the start when Booth is walking after Bones, they walk along and there is no newspaper-stand visible. Camera cuts to in front of the pair and one has appeared in the background that should have been visible in the previous shot. (00:04:10)

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The Parts in the Sum of the Whole - S5-E16

Continuity mistake: In this episode, Booth and Bones are telling Sweets about their "real first case" together - the case where they actually met for the first time. During this episode, Booth, Bones, and Angela take some evidence to Caroline, and Booth introduces them both (most importantly Brennan) to Caroline. However, in season 1, episode 19, "The Man in the Morgue", (which would have taken place after this initial first meeting) when Brennan is accused of murder in New Orleans, Booth has Caroline fly to NOLA to be Brennan's lawyer, and he introduces the two of them. If they had already been introduced during the first case Booth and Brennan worked on together, they would not have needed to be introduced here; they would have already known one another.

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The Dwarf in the Dirt - S5-E7

Trivia: At around 5 mins 11 seconds into the episode, Vincent Nigel-Murrey and Dr. Saroyan are discussing the bones on the forensic platform. In the background of a shot of Vincent, the x-ray on the screen is of Homer Simpson's head in the middle of the screen, instead of a real human skull.

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Question: Between season 2 and season 6 we periodically meet a serial killer called The Grave Digger who's actual name is Heather Taffet. Having watched the complete series a while ago, one thing was never made clear (or I might have missed it) How did Taffet physically bury the containers her victims were in? The twins were buried in a park in a submerged beer vat that is stated as being 6ft high. Bones and Hodgins are buried around 4ft underground in a car. How does she manage to bury them without being seen or interrupted?

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Answer: Answering my own question here but, having contacted various people involved in the production of Bones including Kathy Reichs, Hart Hanson, Eric Milligan, and Deirdre Lovegood who portrayed Taffet onscreen I finally have the answer. No-one know how she did it due to her constantly working alone. And she never revealed this information before her death.

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