Plot hole: The main reason the antimatter bomb was not found, according to the book, is because it is small enough to be hidden anywhere. However, there was a wireless camera watching the bomb all the time. The wireless camera, just like any wireless device, is basically a radio transmitter and receiver, so all they would need is a device displaying the signal strength coming from the camera (having no such device, the CERN could probably borrow some). Where the signal is the strongest, there is the bomb. It is improbable that there wasn't a single person understanding how wireless devices work.
Plot hole: When Julius is going after Pompey to Asia Minor and he reaches the harbor in Greece he tries to talk to the sailors but they don't speak Latin. So he asks Adán to translate for him, but he is unable to since he hasn't learned Greek yet. But Julius is fluent in Greek himself, he was taught as a boy and uses the language on several occasions throughout the series, including in this book. Why couldn't he just talk to the sailors in Greek himself?
Plot hole: When the time stop is almost over, Root uses his "finger" to render Cudgeon unconscious. However, later in the book it is explained that if you lose your consciousness during the time stop you would immediately jump to the end. Cudgeon should have disappeared, and Foaly (or someone else) should have realized how Artemis planned to escape.
Plot hole: Early on in the book the NSA is described as a top secret agency, an agency very few Americans know exist. However throughout the rest of the book there are many references to groups who openly protest against the NSA, bad widespread publicity, and the majority of Americans being against the agency. If hardly anybody knows about the NSA then how can there be so much open debate about it?
Plot hole: The whole premise for Taylor's being forced to go on the lam with her daughter is that she doesn't have anywhere to go - she can't go to her mother Alice's, since Alice is leaving her husband (i.e, Taylor's stepfather) and so this seemingly makes that house not an option. But it's stated specifically that it's Alice's own house Harland moved into - so it makes no sense at all why Alice can't either go back to her own house, or kick her soon-to-be ex-husband out, or have Taylor share the house with her soon-to-be-ex-husband. It makes no sense except as a plot device.
Plot hole: When Lowrie first shows Meg his wish list, she says that they would have to travel the length and breadth of Ireland to complete them. However, she doesn't know what two of them mean so how does she know that they're going to travel that far.
Plot hole: When Phelan Kell is testing to become a Wolf Clan mechwarrior, his Dire Wolf's cockpit takes a hit from a Clan PPC. He continues to fight despite his cockpit now being in open air. In the Battletech universe, a cockpit hit from a Clan PPC is instant death.
Plot hole: On a couple of occasions the book states that It got Victor and Belch at the same time, and that Henry only barely escaped. And when the remaining losers go down to the sewers again they find their two bodies together. Yet during the narrative of the young losers in the sewers Victor is killed early on, and Henry and Belch continue chasing the seven kids for quite some time before Belch is killed.
Plot hole: Virtually all editions of the book have been abridged by removing one chapter of the section during which Huck and Jim are rafting down the river (this chapter is known as "The Raftsmen Passage"). While the chapter in question does indeed slow the story down, it also reveals several key points of information, notably Huck and Jim's location on the river. In the following chapter, Huck is aware of this information. With the "Raftsmen Passage" removed, he would have had to have picked it up by telepathy, as there is no mention of him leaving the raft or otherwise having any source for his information.
Plot hole: On page 56 of the original UK edition, Harry overhears a witch complaining about the price of something as being "seventeen Sickles." There are seventeen Sickles to a Galleon, so a witch who is familiar with the Wizarding world (as she obviously is, given that she knows that price to be unusually expensive) would say "one Galleon" instead. This was changed to "sixteen Sickles" in later editions for this reason. Page 72 in the American version.
Plot hole: At the end of the book you are told that Artemis' father cannot remember anything that happened after he left on the fowl star. Yet in the third book, during one of Artemis's diary extracts he talks about when he was a prisoner - how does he remember that?
Plot hole: When the two boys grow older they set aside their first name and go by their second. Gaius was called Julius instead while Marcus was called Brutus. This is however inconsistent. Gaius full name was Gaius Julius Caesar and Marcus' was Marcus Junius Brutus. They should either have been called Caesar and Brutus or Julius and Junius, not Julius and Brutus.
Plot hole: Spiro's vault can only be opened by Spiro himself, but the guards change every hour and Spiro doesn't go to the vault every hour of his life to let the guards in, so how do they get in?
Plot hole: When Neptune places the curse on Emily, her hands begin to become webbed but never once does she have webbed hands when she is a mermaid so the curse shouldn't cause this. She isn't becoming something that she isn't, she is becoming half mer half human, so the curse shouldn't affect her hands because they never actually transform when she changes into a mermaid, only her lower half changes. Even the pictures in the book show hands that aren't webbed when in mermaid form.
Plot hole: In the first chapter, when Bridget is going to Grafton Underwood for the Turkey Curry Buffet it's is clear that she drove there - she mentions getting onto the M6 by mistake and jamming her foot down on the accelerator - but towards the end of the buffet, Mark is made to offer her a lift back to London, to which she replies that she will be getting the train back in the morning. Surely she would just drive back? What would be the point in leaving her car at her parents' house?
Plot hole: In Chapter 8, Oliver examines a dead body which has a nightstick fracture of the right forearm bones. While examining the fractures, he discovers a pierced olecranon fossa - a hole through the bony elbow joint - of the same arm. When his examination of the other arm reveals that it does not have the same hole, he realizes that the hole in the right elbow socket must have resulted from wear and tear - specifically, the repetitive snapping motion of pitching a baseball - since birth defects are usually bilateral. This in turn leads him to identify the dead man as a former baseball pitcher who quit playing when he wore out his arm. The problem? Throughout the book, the man is referred to as "left-handed" and a "southpaw" pitcher. He pitched left-handed, so he should have worn a hole through his left elbow socket, not his right.
Plot hole: When Fireheart takes Cinderpaw out to see the borders for the first time, when they reach the Shadowclan border Cinderpaw says: "I remember that scent from when Brokenstar attacked our camp. And it was on the kits he took, when you brought them home. It's Shadowclan!". Cinderpaw implies that she wasn't one of the kits that was taken, but she actually was. In Into the Wild, when the kits are being rescued, it says: Firepaw helped Greypaw to lift out the rest of the kits. The last one was grey, like the embers of an old fire. She mewled." This kit is female, grey, one of Frostfur's (like all the others that were taken) and is the right age to be Cinderpaw.
Plot hole: (Spoiler alert!) At the end of the first part ('Search by the Mule'), when the Mule, Channis and Pritcher are on the planet Rossem, the Mule says he had to follow Channis because Channis is an agent of the Second Foundation, and as such, has the ability to resist the Mule reading his mind. Yet, at the end, when the Mule's ships are bombed Tazenda, just before the First Speaker arrived, the mule forcibly made Channis tell where the Second Foundation is (that is, what Channis thought about the whereabouts of the Second Foundation). Now how come that Channis couldn't resist the Mule on Rossem, but he could on Kalgan? The Mule was much more powerful than Channis on either planets.
Plot hole: When Angela and Brom met in Teirm they did not appear to have ever met before. According to Jeod, when his character very first appears in the book, Brom has not changed since the last time they saw one another, quite a few years ago. Later on when Eragon is talking to Angela in her shop Angela says that shes a lot older than she looks. Nearing the end of the book, when Eragon and Angela are talking in her room, when Angela explains how she came to be in Tronjheim, Angela says that she met Brom once. But if neither of them has aged very much surely they would have recognised each other in Teirm?
Plot hole: The arms dealer tells Special Branch detectives that Charles Calthrop - wrongly suspected to be The Jackal - barely escaped with his life when Rafael Trujillo, the dictator of the Dominican Republic, was assassinated in 1961. "The whole regime collapsed within hours." He tells them, relating how Calthrop was with the Police Minister at the time and had to flee, bribing a fisherman to take him off the island in order to escape the angry mobs of partisans who were rioting in the streets, indiscriminately killing anyone they thought had collaborated with Trujillo's regime. What cobblers. There were no partisans and no riots. Trujillo's regime continued uninterrupted. His brother Hector immediately took power and ruled absolutely and ruthlessly for another eight years. Calthrop would have nothing to worry about unless Trujillo himself had signed his pay cheque. Calthrop's alleged involvement in the assassination is a hugely important plot point as it inadvertently leads to the discovery of the false passport obtained by the Jackal and the uncovering of his false identity, and his name was only placed on file because of his rumoured involvement in events which simply did not take place.