Alternative Character Interpretation: The first book deliberately aims for this by making sure that every time Artemis does the right thing, he can explain it away as Pragmatic Villainy. The psychiatrist who narrates the book argues that Artemis is a sociopath (though admittedly not a standard case by any sense of the imagination), and warns of the tendency to view him as more noble than he really is. Later books make him more of a hero, though.
Him becoming a hero is explicitly stated to be character development. In the Eternity Code, just before the mind wipe, he says that he might become the monster seen at the start of the series. The next book reveals that he was right.
Anvilicious: Book 6: Go green, and you'll save the krakens, stop poisoning fairies with Spelltrophy, and keep the world from dying. Plus, Artemis Sr. puts emission filters on every vehicle they own, including the jet and helicopter. Though the series has dropped environmental anvils all over the place since its beginning.
Technology of the series doesn't appear to have any consistency: numerous vital plot points happened just because fairy technology happens to be capable to do something we weren't informed of or has a limitation never brought up before.
One short story in the companion book is set in the period between the first and the second book, aka when Artemis was still a egoistic criminal mastermind and Mulch was believed to be dead by the LEP. Holly goes to stop Mulch in his tracks, but she isn't supposed to know Mulch is even alive... Well, let's make him wear a mask! Voice? Did we mention all the dwarves' voices are exactly the same and even the dwarves themselves can't tell one from another? Because now they are.
Dwarf biology can generally be relied upon to produce one new secret trump card for Mulch to get out of trouble with each book.
Magic has a bunch of new rules too: Grease is toxic for people with magic in them, animals can get glands extracted to enhance power, runes only need one spark to do something powerful wizards can't and mesmerizing on the fair folk works except when it doesn't.
The first book mentions that Butler's family are all trained at a school in Israel but Butler later remembers something from the Swiss academy. Eternity Code explains that the school moves every five years and that Butler spent the first few years in Israel until it moved to Switzerland.
Mulch somehow uses the Gift Of Tongues to talk to some dogs in Arctic Incident even though he's lost his magic. Lost Colony handwaves this by saying both Mulch and Doodah Day each have a spark of magic left that lets them use the gift. Sadly this is contradicted by Atlantis Complex that says Bobb Ragby can't use the Gift since he lost his magic and Mulch implies he had to learn English.
In the Disney graphic novel, Butler asks Artemis why they didn't just kidnap the fairy healer from Ho Chi Minh city and Artemis replies that The Book says that fairies who drink with humans are considered excommunicated and nobody would pay her ransom.
Opal Koboi is a genius pixie who desires to become "empress of the world". Opal before the series became head of her father's company by driving him insane and having him and her mother locked in an insane asylum. Organizing the Goblin rebellion alongside Briar Cudgeon, Opal took advantage of their violent nature to cause an uprising, while all along planning to betray them. To escape prison after being arrested, Opal creates a clone, not caring it will die easily and cannot think for itself, allowing her to manipulate it. Killing Holly's mentor, Julius Root, by having a bomb strapped to him and then cruelly tricking Holly into detonating it, Opal then frames her for it and Mind Rapes a kind-hearted humanitarian, forcing him to send a probe into the Earth and reveal the Faerie people, hoping to cause a war behind humans and Faeries. Opal is also revealed to have experimented on and killed endangered animals to make herself more powerful. In the final book, Opal murders her own past version of herself when the past version of her was trying to free the present Opal from prison, which causes all products produced by her company to explode, with planes crashing and global communications cutting off. Finally, Opal manipulates the ghosts of dead Faeries to Kill All Humans and take over the surface world. A thoroughly childish woman dedicated to getting whatever she wants regardless of innocent lives lost, Opal is Artemis's greatest and most evil enemy.
Lost Colony: The demon Leon Abbot, real name N'Zall, was a bellicose proponent of demonkind's war with mankind even when it meant certain extinction for their race. Sabotaging a ritual by the demonic warlocks to save their people to kill the warlocks, Abbot returns to the demons, pretending to be a savior while brainwashing the masses into thinking they were resuming their war with humanity, with Abbot instead using it as a ruse to keep them under his control. Savagely torturing any who show opposition to his power, Abbot remains apathetic even when Artemis and his allies reveal that Abbot's methods will lead to the destruction of his dimension. Causing the extinction of his people before time is reversed, Abbot again tries to kill the heroes even after being brought back to life, endlessly bitter and power-hungry.
Die for Our Ship: Depending on whether you ship Hartemis or Artemin, either Minerva Paradizo or Holly.
Homage The ending to The Eternity Code is suspiciously similar to that of Dead to Rights, which came out a year earlier.
Idiot Plot: The entire berserker threat would never have occurred if they had simply killed the future Opal BEFORE they put her in the reactor tank.
It is admittedly implied to be a result of fairy society being based off of Actual Pacifism, so that they are neither legally allowed nor morally inclined to shoot a prisoner. Although that explanation doesn't make much sense given Artemis and Butler were also present and seemingly neither of them even thought of it.
They were present in the control room in Haven, not the cell block in Atlantis. They could suggest it but not do it. They probably did think of it but knew there was no point saying anything.
The Atlantis Complex: For starter said complex is pretty much how you glue the Idiot Ball on Artemis, the elven space project being accessible by a prison guard (and existing) and no one but Turnbull and the old fairy in Vietnam knowing about the magic spark trick.
Not to mention all of the people in cities who will starve to death because they can't get food shipped in, submariners who are trapped in steel tombs miles beneath the waves, miners stuck in shafts with no way out, and anybody on a boat, who will be most likely stranded in the middle of the ocean. The book also stated that anything connected to Opal Koboi, exploded, which includes most of our modern technology, such as pacemakers. But hey, at least people aren't distracted by TV anymore!
Justified: the narrator ends up being Holly Short, a fairy, so it makes sense as to how she wouldn't dwell on the human deaths.
Unintentionally Unsympathetic: Turnbull got a Cry for the Devil before dying with his loved one but the guy has the highest bodycount after Opal, brainwash people and was first introduced torturing an officer for another petty scheme. Only reason why Artemis would say he can't see him as a villain is because he is unaware of most of it because he was too busy guilt-tripping. Even his relationship with his loved one isn't that great when you keep in mind he brainwashed her into staying with him forever.
The Un-Twist: In the first chapter of The Last Guardian, Dr Argon ominously wonders if it is really possible that Artemis has been cured of the Atlantis Complex in record time. He has, and the only thing we hear of the Complex for the rest of the book are a few fleeting mentions.
Though it does seem to have badly damaged his self-confidance.
Values Resonance: Despite being said in his time as a mob boss, Artemis Fowl Sr's line about buying gold as a reliable investment and keeping it safe seems far more resonant in modern times.
Butler and Juliet receiving a Race Lift by being played by Nonzo Anozie and Tamara Smart, even though they were explicitly Eurasian in the books. Part of the negative reaction to this is due to the Butler family being cast entirely as dedicated guards, servants and aides to the Fowl line, and some felt that casting a black man for this role sent... rather Unfortunate Implications.
Lara McDonnell as Holly Short. The actress didn't have nut-brown skin, nor was she older than Ferdia Shaw, who plays 12-year-old Artemis.
The most criticized is Judi Dench... as Commander Root. While the actor has already been praised in other roles beforehand, especially as an Iron Lady, people still felt that changing Root's gender kills the dynamic him and Holly shared in the books. The source material had Holly as the first female LEP Captain, Root being strict to her because of this uniqueness, and Holly herself being under a great deal of public and internal pressure to serve as a model for future female officers. Having a female Root as the already well-established leader of the LEP is largely incompatible with that particular angle.