Alternative Character Interpretation: While it's pretty clear Asmodeus' "love" for Bane is nothing but unhealthy and manipulative, is he just pretending to love his son so he can use him to his own ends, or does he genuinely believe, in his twisted logic, that he is a doing what is best for him?
A complaint of the first book was that the parabatai bond was very much an Informed Attribute, leading to Cassandra Clare having to use the second book to put emphasis on it. The series puts more emphasis on it.
Some fans are annoyed at how Clary keeps forgetting Simon in the books. The TV series goes out of its way to give them more scenes together, and to lampshade how hard it is for the two of them to find time for each other.
A few felt that Clary veered into Damsel Scrappy territory in the books. The TV series gives her plenty of moments that establish her as an Action Girl; case in point: Jace killed the demon in the apartment in the book, whereas in the show, Clary does it herself.
An adaptation change some didn't like was that Maryse had a strained relationship with Isabelle in Season 1. In the second half of Season 2, an episode revolves around them repairing their bond.
Bizarro Episode: The seventh episode of Season 2 received huge backlash from fans who felt that the episode felt too disjointed from the rest of the series, with none of the characters acting in character bar Simon and Luke. With Jace purposefully giving Simon abysmal dating advice for seemingly no reason, Clary tasering her father figure Luke after refusing to listen to his orders, and a dubiously-consenting sex scene between Magnus and Alec which lead to many of the writershaving to respond to the controversial scene, it's understandable why many fans felt deceived. It becomes even worse when, the week leading up the episode, was specifically referred to as "Malec Mania"...only for them to have three minutes of screentime in said episode.
Isabelle becoming Hotter and Sexier. There have been blog posts complaining about it, accusing the show of objectifying Isabelle and turning her into a sex toy. There were a few complaints about the scene of her sleeping with Meliorn to get information, too. Others are fine with it, finding it's not that drastic a change and citing that Isabelle still gets more characterization beyond being Ms. Fanservice.
Katherine McNamara as Clary is a polarizing casting choice, especially since she had most played Alpha Bitches before. There are constant debates over whether she's one of the weakest or strongest members of the cast.
Dominic Sherwood is almost as divisive a casting choice. Some fans love him and feel he captures Jace perfectly, while others find his delivery to be way too forced and over-the-top (evidence by most of the Narm examples below being provided by him).
Whether Season 1 or Season 2 is better. Many fans think Season 2's more mature tone is a great improvement, while others think it's too dramatic and miss the more lighthearted tone.
Whether the changes from the books are an improvement or a travesty.
The Seelie Queen quickly became one when she appeared in the second half of Season 2, thanks to a fun actress playing her (fans usually prefer Lola Flannery to Sarah Hyland, though) and how she established herself as a Magnificent Bitch with the stunt involving "the kiss you most desire").
Fanfic Fuel: There have been many fanfics written that take place in the alternative universe in 1x10.
Fetish Retardant: The scenes between Isabelle and Raphael during the former's addiction. The fact that Isabelle is essentially getting high and feeding her addiction prevents the scenes from being completely sexy.
Growing the Beard: Fans of the show point to the fifth episode "Moo Shu To Go" as a marked improvement. The actors settle into their characters better (especially Emeraude Toubia and Matthew Daddario), effects get a little better, and the episode structure is better. Season 2 is also viewed as a massive improvement for its Darker and Edgier tone, with both acting and special effects getting much better, too.
Harsher in Hindsight: Sarah Hyland was cast to play the Seelie Queen. There was a lot of backlash because she was dating Dominic Sherwood (Jace) and many people thought that she got the role solely for that. As of August 2017, Sarah and Dom broke up, with many fans speculating that her guest-starring on the show was what tore a wedge between the two of them. Not helping matters was that the Seelie Queen tries Relationship Sabotage in her first appearance (although she's played by Lola Flannery in that episode).
Clary and Izzy have a much more loving relationship in-show than they do in the books. Aside from just being generally nicer to each other, they also get a lot of sweet and touchy moments, with Isabelle brushing Clary's hair back, holding hands, and staring into each other's eyes, etc.
Isabelle: Do you think red's my color?
Clary: With a body like yours, Iz, anything's your color.
Magnus and Ragnor, as well. They've been close for centuries, as evidenced by their Like an Old Married Couple routine, and when Magnus thinks Ragnor's been poisoned, he begs him to stay and kisses his fingers quite tenderly.
The flashback scenes in "Of Men and Angels", as the actress playing young Jocelyn looks almost nothing like her (wearing a very obviously fake-looking red wig), and her line delivery leaves a lot to be desired.
Jace and Clary's first meeting. Viewers erupted into hysterical chuckles over Dominic Sherwood's ridiculously dramatic delivery of "You have the sight?"
Alec has to strip off to use the parabatai bond to track Jace. It's not explained very well (he has to access the runes on his body), so it looks like Matthew Daddario has gone rogue and is trying to throw some gratuitous shirtless-ness in there.
Jace is a veritable fountain of Narm whenever he interacts with Simon. Particularly when they get into a fight in the third episode and Jace calls him "Mundane" in the most forced way possible. Their rivalry isn't conveyed very well and feels way too forced to be anything but laughable.
When Aldertree is describing The Lost Lenore to Alec, he takes the time to list her as "sexy". An odd way to describe the deceased woman he loved, and it's bound to incite chuckles in what's meant to be an emotional scene.
In the Season 3 premiere, Luke says the following line to Clary without a hint of irony ("You don't choose the blades; the blades choose you") and she doesn't lampshade the cliched-ness of the saying.
Never Live It Down: Isabelle sleeping with Meliorn to get information is something that's frequently brought up, despite it happening very early on in Season 1.
One True Pairing: Alec and Magnus. Fans who hate the series otherwise declare that their relationship is the only reason they watch it.
Special Effect Failure: The CGI to simulate portals looks very cheap, like a first-time attempt on After Effects.
One of the biggest complaints is that the Institute changes drastically from book to series. In the books, the tracking was done entirely with magic and runes. The TV series portrays it as more high-tech with computers and other gadgets, giving it more of a Science Fantasy vibe. Cassandra Clare even says she isn't a fan of this change since she envisioned the Shadowhunters being anti-technology most of the time.
The show has received some complaints about Clary's Adaptational Attractiveness. In the books, she's an awkward teenager who doesn't like dressing up. In the series, she's a confident young adult who is just as gorgeous as Isabelle. There's a scene where Izzy says she wishes she was as flat-chested as Clary, which doesn't make sense considering Katherine McNamara is just as well-endowed as her.
The toning down of the BrotherSister Incest storyline from the books. Jace and Clary struggle with their feelings for each other for a whole book, and the "kiss you most desire" happens while they think they're still related. The show's decision to reveal they're not related much earlier was viewed as a cop-out by many.
Testosterone Brigade: Katherine McNamara and Emeraude Tobia are gorgeous, and the show unabashedly shows off their beauty in every episode (though Isabelle does go through a phase where she dresses more modest to please her parents). As a result, many male fans watch it just for Clary and Isabelle. The second half of Season 2 also ages up the Seelie Queen and gives her a Hotter and Sexier outfit.
The Un-Twist: Even for those who didn't read the books, it was very obvious that Michael Weyland was Valentine in disguise. The fact that Valentine inexplicably vanishes when he's found, and Michael acting contradictory to the way Jace described him makes it obvious he's an impostor long before Clary figures it out.