Anti-Climax Boss: After all the build-up about how she is one of the worst witches ever, Mother Malkin ends up killed quite easily the two times she confronts Tom. To add insult to injury, her final death is being eaten by pigs.
Also, Mistress Wurmalde, who after acting as the major antagonist of most of the book and being called an immortal, is unceremiously killed off by one of Tom's lamia aunts. Lampshaded by Gregory.
Elizabeth of the Bones, commonly known as Bony Lizzie, is a sadistic child-killing witch who harvests bones for rituals. Posing as Alice Deane's aunt, she's actually her mother, having conceived with the Fiend. She once had a brain-eating familiar, and Lizzie didn't interfere when it targeted her daughter. She first plots to free her dreaded grandmother Mother Malkin by tricking Tom into giving her blood cakes and abducting a little boy as a meal. She inflicts Tom with nightmarish hallucinations, before she tries to take his thumb bones. After taking over the isle of Mona, she murders a miller who challenged her authority, trapping his soul in limbo, sentences John Gregory, Adriana and Commander Stanton to be fed to the Buggane, drinks the blood of a yeoman and leads raiding parties slaughtering entire families. When Alice ruins her plans of world domination, she attempts to take her life then successfully kills Adriana and her fiancé. The flashback of the twelfth book reveals that she killed a Spook before torturing his soul and attempted to kill thirteen children for a ritual, while in the present day, her ghost ambushes Alice and Thorne to be interrogated and tortured by the daemon Beelzebub. In The Dark Assassin, Lizzie treacherously delivers the witch assassin Grimalkin and Thorne to another daemon.
Bill Arkwright is abusive toward Tom and relies on drastic methods to deal with creatures of the Dark, but considering his whole family died and ended up as ghosts trapped in his home with him unable to help them, you have to feel sorry for him.
Paranoia Fuel: In book eight, The blood jar getting weaker throughout the book.
Strawman Has a Point: Thomas thinks Bill Arkwright is cruel to give witch hearts to dogs instead of making jails like Gregory. However some would consider it better to eliminate evil for good than keeping potential threats around.
What Do You Mean, It's for Kids??: The books generally have a recommended age group of "10 and up". Considering the amount of violence and dark material (particularly in the later novels), however...
Alice has been raised for most of her childhood by her aunt (who is actually her mother who temporarily abandoned her then took her back as an apprentice) Bony Lizzy, who was ruthless with her, forced her to learn black magic against her will, and injured her just so she could use her blood. When she finally escapes this life by befriending Tom, she is moved to another nicer aunt only to have this aunt die by the next book thanks to the Inquisitor. She is then allowed to live with Tom and Gregory for a while, but Gregory refuses to trust her and threatens to throw her in the pit should she ever show signs of joining the Dark. Come Book 8, the Fiend takes her to his Realm as a punishment for helping Tom, and though he manages to save her eventually the torture she goes through leaves her with huge trauma. And to make matters worse, Book 10 reveals the only way Tom will be able to defeat the Devil for good will be by sacrificing her, because she's the being he cares about the most.
Judd Brinscall in Book 10 fell in love with a woman he met during his travels and was about to marry her only for the woman to be possessed by a strigoica (and this kind of possession is irreversible). He tried to chase the strigoica to avenge his loves loss, only to end up captured, reduced to a living food supply by them and forced into betraying his former master Gregory by luring him into a trap. When he is freed by Tom, the boy understandably has a hard time trusting him or forgiving him even though he is more than willing to make up for it. Then he ends up killing the Strigoica who possessed the woman he loved, forcing him to not only kill her but also brutally mutilate her body to ensure she wont be possessed again. And then the body ends up possessed again anyway by a vampire god, forcing him to kill it again.
Anti-Climax Boss: Malkin does have a big fight... against Bony Lizzie, who she defeats. After that, she is easily killed by Tom using a knife.
Cliché Storm: A prophecy that can only be fulfilled by The Chosen One? Check. Medieval Europe setting perfect for a fantasy adventure? Check. An evil and one-dimensional villain with mundane goals and a strong preference for black and red robes who lives in an evil lair? Check. An ordinary farm boy who's swept up in a grand adventure full of magic and wonder to defeat an evil overlord with the help of his friends? Check. An old wizard who takes the hero under his wing to be his apprentice with a tendency to speak in riddles? Check. A generic love interest who's a Flat Character and betrays her evil overlord to assist the heroes? Check. A magical object that the heroes must protect lest it fall into the wrong hands? Check.
To be slightly fair, the source material was also guilty of some of these cliches as well, but it's no wonder that the film bombed as massively as it did. Audiences and critics alike were reported to have been disinterested from just the trailers and the synopsis alone because the film is presented as a run-of-the-mill fantasy adventure film with nothing that makes it stand out from the rest of its ilk.
Evil Is Sexy: The evil female witches are dressed in somewhat provocative clothing, with Bony Lizzie in a tight corset and Mother Malkin in a flamboyant black outfit complimented by huge eyelashes and black eye shadow. The good witches wear plainer-looking attire.
Misaimed Fandom: The film was doomed for failure when you realize that it had no audience to hope for to rake in the cash, in addition to being placed in a dump month for release, which is a pretty big red flag. The fans of the novels were already pissed off at all of the creative liberties taken with the source material, to the point where it barely resembles the first book, and the trite and predictable plot was also a turn-off for the general audience with the groan-inducing cliches and tropes present in just the trailer alone. This film had no hope for success.
Stillborn Franchise: The open ending certainly left room for at least one more sequel, despite how much different this film is from the first book (this was because the film cobbled together several elements of the novels into one), but the disastrous box office and pitiful reviews pretty much doomed any possibility of a potential franchise. It's nothing the book's fans would be complaining about though.
Strangled by the Red String: Tom and Alice share two scenes before they kiss and confess their love for each other. In the books, it takes several novels before Tom acknowledges he might have feelings for her.