The Shadowhunters: Guardians of humanity, or racist, elitist snobs?
Captain Obvious Reveal: The series is rather infamous for these, due to its very obvious use of Foreshadowing. The most hated examples were that Valentine was Clary's father and Clary and Jace weren't siblings.
Damsel Scrappy: Clary mostly. Indeed, Simon would be leading a happily mundane life were it not for his determination to protect her even though she just sees him as a friend. Jace could be argued as being a male version of this trope as well, since a great deal of effort on the part of Clary, Alec, Isabelle, Magnus, the Lightwoods, and others centers on saving him from some life-threatening situation that could have been avoided were it not for his nasty independent streak.
Poor Aline. She consensually kisses Jace once, while he and Clary are still convinced they're siblings, and promptly decides that he's not her type, is a fairly kind person overall (albeit one with no brain-to-mouth filter), and it's implied that she's trying to figure out if she's a lesbian, or perhaps asexual - yet she is constantly turned into a cruel, backstabbing, relationship-smashing harpy who gets between Clary and Jace, especially in AU fanfics.
The release of City of Lost Souls helped the problem a little - it was confirmed that Aline was lesbian, and none of the characters felt any hatred to her.
Kaelie gets this treatment too even though she only appeared twice and doesn't show any interest in Jace at all. Usually in AU's she gets the same treatment as Aline, in series we know that Faeries don't care much for humans.
Draco in Leather Pants: Sebastian gets this in many fanfics where his actions are at best given a poor Freudian Excuse and he is made a badder bad boy than Jace so they can have a love triangle. He was forced to do it by Valentine and/or was abused crops up a lot as an excuse. Other times writers will have him say he can't control himself or at worse ignore that he killed a child or completely hand-wave it. Some writers go as far as trying to make Jace a Ron the Death Eater by having him be a bigger jerk than usual to make Seb seem nicer.
Faux Symbolism: In City of Heavenly Fire, Sebastian leans over and kisses Jace on the cheek. Later on Jace explains that Judas did the same to Jesus to identify to the Roman solders who Jesus was. However the situation in the book has literally no parallels to the situation with Judas and Jesus.
Foe Yay: In one scene in City of Heavenly Fire Sebastian leans in and kisses Jace's cheek. It's meant to be a threat and parallel to how Judas kissed Jesus' cheek to identify him, but it comes off a bit like this.
Jace and Simon have a fair amount of subtext. Especially if these two quotes have anything to say about it:
Jace: "Do you remember back at the hotel when you promised that if we lived, you'd get dressed up in a nurse's outfit and give me a sponge bath."
Clary: "It was Simon who promised you the sponge bath."
Simon: "As soon as I'm back on my feet, handsome."
Jace: "I knew we should have left you a rat."
"Well, I'm not kissing the mundane," said Jace. "I'd rather stay down here and rot."
"Forever?" said Simon. "Forever's an awfully long time."
Jace raised his eyebrows. "I knew it," he said. "You want to kiss me, don't you?"
Near the climax of City of Ashes, Jace allows vampire-ified Simon to drink his blood in order to heal. This results in Simon with his arms flung around Jace, clutching him violently, and biting his neck. Furthermore, Jace explicitly relaxes and pulls him closer. Uh...
Jace later admits that it was rather homoerotic, and that he did in fact like it just a little bit.
When she sees Magnus and Alec kissing, Maia asks Isabelle "do we have to do that?"
Narm: It can be rather hard for a reader to take a villain named "Valentine" seriously.
Portmanteau Couple Name: Quite a few. Most popular is Malec (Magnus/Alec), as well as Clace (Clary/Jace) and Sizzy (Simon/Izzy). And that's just the canon ones.
Rooting for the Empire: The designated heroes, the Shadowhunters, are descended from the angel Raziel—and pretty damn proud of it. They see themselves as above the very people they're supposed to protect: Downworlders (your werewolves, faeries, vampires, and such) and humans, otherwise known to Shadowhunters as Mundanes (or Mundies, if you want to get really ugly). Honestly, with this sort of Fantastic Racism, you'd probably get more love and respect from a demon disemboweling you and dragging your soul straight to Hell; at least demons are supposed to be cruel. To be fair, the Shadowhunters are called out on this all the time by everyone who isn't a Shadowhunter. The moral of the first 3 books is that the Downworlders aren't inherently evil and the Shadowhunters aren't inherently good and that they could save a lot more lives if they got over their differences and helped each other. Indeed, City of Glass ends with the Downworlders agreeing to help the Shadowhunters defeat Valentine in return for the Downworlders getting representation in the Shadowhunter's council.
Ship Mates: Fans tend to support the canon Alec/Magnus and Clary/Jace ships, seeing as that takes care of Alec's crush on Jace from early on in the series and leaves Jace wide open for a romance with Clary.
This is a pretty sensitive issue to a lot of people, so we won't go into too much detail. But there's a not-insignificant number of people who accuse Cassandra Clare of plagiarizing several other works, most notably Harry Potter and Star Wars.
There's actually some logical basis in this - Clare copied large amounts of texts from other sources without citing them in The Draco Trilogy: a Harry Potter fan fiction she wrote before City of Bones was published. In fact, the fics were taken down and the trilogy is largely a reworked and renamed version of the fic. Her fans argue that Clare learned her lesson from that, and that the elements Clare is accused of copying weren't invented by the people she 'copied' them from.
Unpopular Popular Character: Simon is constantly mocked and belittled by the Shadowhunters for being a "mundane", no matter what he does. Even Clary, his childhood friend and love interest can hardly be bothered to remember him most of the time. A number of fans, especially those not overly fond of the Shadowhunters, love him for his snark, adorkable geeky personality, and willingness to do nice things for Clary. It helps that he's one of few not afraid to call out Jace on being a jerk.
The main character, Clary, witnesses a boy her own age tied up (with piano wire) and questioned by people talking about demons and accusing the boy of being one, going so far as to threaten to kill him with a knife. You'd Expect: Her to leave immediately and look for a bouncer. Instead: She stands and watches, and then steps in when one of these obviously deranged people brings out a knife.
Soon after, the tied up boy attacks one of his captors, who kills him, and the boy's body basically implodes into nothing. His kidnappers and murderers continue to say he was a demon, and when her friend and a bouncer arrive she is apparently the only one who can see them. You'd Expect: Clary to seriously question whether or not she was sober at this point, considering she was in a club, and these people keep talking about magic and demons, and you know, she's the only one who can see them. Instead: She seems to accept what these murderers are telling her, and seems to think her doubts are wishful thinking.
After leaving the club, Clary's Childhood Friend Simon asks her if she's alright. He obviously knows something is wrong with her, and keeps asking her if she has something she wants to tell him. You'd Expect: Clary to confide in Simon, whom she's known for ten years, since what just happened was so traumatic. Instead: She doesn't tell him anything at all, her reasoning seeming to stem from how the MURDERER Jace talked to her.
The next evening, when talking to Simon in a resturaunt, Clary spots Jace again when he interrupts her conversation with a snort. He's armed, she's already seen himkill someone, and Simon is obviously trying to tell her something important. Jace, after interrupting her conversation, gets up and leaves. You'd Think: Clary would stay with Simon, perhaps very disturbed that her hallucination is appearing again, and maybe tell Simon what she just saw. Instead: She runs out after Jace. Jace, who she saw kill someone. Jace, who has a knife very like the one he killed someone on him at this very moment. Jace, who apparently only she can see. She runs after him outside. At night. "Terrified that he would disappear like a ghost." And she doesn't say a single word to Simon. She just up and leaves.
Jace Wayland, he was abused as a child and believed for some time that he watched his father die matters only become worse when he finds out that his father did not die but abandoned him and is actually a famous villain in his world, Valentine which means he is siblings with the girl he loves. Because of some mistakes in genealogy, he believed that his mother abandoned him and thought that he was a monster. Later he finds out that he has demon blood in him which would mean he was a monster, though this proves to not be true. Also, he is betrayed by a friend Hodge and handed over to the villain. He was arrested for insulting the Inquisitor, was kicked out of his house and left with no where to go and arrested by the Inquisitor again, who planned to trade him to Valentine for some powerful Shadowhunter relics, and because almost everyone assumed that he had joined the evil side. He is also killed by the man who raised him, though Clary brought him back to life.
Alec Lightwood. He's gay and the member of a race of people who... aren't exactly accepting of it. As a result, he's too afraid to come out to his parents. Not only that, he's in love with Jace, who will never love him the same way, and is so hung up on this that he doesn't even notice when a certain warlock does. Luckily, things work out for him in the end.
Opinion Myopia: Many either think the film failed because it was a half-assed Twilight ripoff or think it failed because Twilight was so bad that it poisoned the well for other, better supernatural young-adult novels being adapted to film.