These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Canon Sue: Clary has often been accused of being this. The similarity of her name to the author's doesn't help.
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.
Die for Our Ship: 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 possibly even 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.
Ensemble Darkhorse: Clare often expresses her surprise at the fact that many people state Alec as their favorite character as opposed to Jace or Clary.
Isabelle too, for some.
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.
Yeah 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 the second book, 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.
Old Shame: You know, it might be easier for Cassandra Clare to erase all memories of that NC-17 Ron/GinnyIncest Fic if she didn't go and give her published series the exact same name.
And boy, does it ever show on the Amazon reviews.
It would likewise have been easier for her to ditch the whole plagiarism debacle attached to the Draco Trilogy if she'd either used her real name or else gone with a different pseudonym. She's one of the few writers who had a pre-built Hatedom and Fan Wank before she even got published.
But she also had a built-in fandom and she got her book deal because of her fandom fame, so it's a bit of a double-edged sword. The fact that so many characters are Expys from her best-known work, not to mention the copy/paste of scenes from the same into this series, would make it a little hard for her to get away with pretending to be someone else anyway.
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.
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 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, plagiarized sections and all. 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.
The only half-black character in the series, Maia, is characterized solely by how much violent abuse she's taken in the past at the hands of the men in her life. Averted in that she eventually defeats a rather large male werewolf to claim leadership of the New York pack.
At one point Clary notices there are no unattractive vampires, and concludes that "maybe ugly people don't want to live forever." It turned out that the process of becoming a vampire erases visual flaws, which comes with its own set of problems with the othering of people who are at all visually imperfect.