Continuity mistake: When interviewing Lexi she puts her arms up and plays with her hair in one shot but then in the next her arms are down. (00:28:30)
The Doctor in the Den - S4-E18
Continuity mistake: When Booth is questioning Brandon for the first time, Booth and Brandon's positions in the interview room are different to the live feed behind the glass. (00:16:40)
The Salt in the Wounds - S4-E17
Continuity mistake: When lowering the remains into the tank, Aristoo's grip on the remains changes instantly. (00:11:05)
The Princess and the Pear - S4-E15
Continuity mistake: When Hodgins finds the sword the plastic wrap is very wide around the hilt. When he holds the sword up, the plastic is flush with the hilt. (00:20:40)
The Passenger in the Oven - S4-E10
Continuity mistake: When Booth sneaks into 1st class at the start Bones slides her eye mask up on her forehead. A few shots later, without touching her mask, it is now a lot higher on her forehead. (00:02:15)
The Beaver in the Otter - S4-E24
Continuity mistake: When Bones is telling the physics professor that 5 students failed the exam, the professor is clasping up her briefcase. Shot changes and her hand is no longer on the briefcase. (00:22:10)
Continuity mistake: When in the diner after going to the Japanese tea room, Booth has his fingers rubbing his temple. Shot changes and his hand is lowered. (00:11:15)
The Skull in the Sculpture - S4-E8
Continuity mistake: Booth asks Roxy if she used to get the victim his drugs. When he does so, he has his hands clasped together with his index finger raised. When the shot changes, his hands are no longer clasped and the index finger is no longer raised. (00:15:40)
The Doctor in the Den - S4-E18
Continuity mistake: When Angela first walks onto the platform at the start and starts flirting with Clark, the way she holds her folder changes between shots. (00:03:30)
The Salt in the Wounds - S4-E17
Continuity mistake: The way Booth's hands are clasped when talking to Clint at the end in the diner changes between shots. (00:39:00)
Continuity mistake: Hodgins takes the lid off the fish blender twice when trying to find out what killed the fish. (00:32:00)
The End in the Beginning - S4-E26
Plot hole: We learn that Agent Booth has a brain tumor that has been causing him to hallucinate. One of the hallucinations mentioned was Parker in "The Hero in the Hold." At the end of the episode, Dr. Brennan both sees and speaks to Parker in the cemetery. Agent Booth believed Parker to be a ghost, and we were to believe that Dr. Brennan had unknowingly had a paranormal experience.
Suggested correction: The implication of that episode was that Parker's ghost was real, since Booth points out numerous things he does during his escape that he couldn't have done on his own. Dr. Brennan seeing Parker at the end of the episode confirms this. Dr. Brennan is the only one to posit that Booth's belief that he saw Parker was a hallucination brought on by his brain tumor, because she did not learn who Parker was when talking to him in the cemetery; Booth was looking the other way, all Brennan knew was that a young man walked up to her and said something about enjoying life. Even if she saw a picture of Parker at some later date, she probably wouldn't recognize him.
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)
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 Critic in the Cabernet - S4-E25
Continuity mistake: Hodgins and Fisher are discussing how hard it is to remove wine stain. Hodgins' rubber gloves are very dirty. When Fisher realizes how to clean the bones, Hodgins' gloves are much cleaner, only stained around the finger tips.
Factual error: Dr. Wexler is killed in his flat in Oxford, yet the the fire engine outside his property is marked as being from the London Fire Brigade rather than the Oxfordshire Fire and Rescue Service. (00:04:20)