Harry/Cho was swiftly sunken in this book and along with it nearly all of its supporters.
Many people realized that the scene with Harry and Ginny eating chocolate in the library (in the book) was a torpedo heading directly for the Harry/Hermione ship.
Accidental Innuendo: Draco makes a barb saying "we'll be dogging your footsteps" (referencing Sirius turning into a dog). Dogging is a UK slang term for having sex in public places, knowing there are people nearby.
Luna, in the mistletoe scene in the Room of Requirement: Legitimately worried about Nargles, or covering for her dashed hopes that she could finally snag a kiss from someone?
Because of how little characterization she had, Marietta Edgecomb is subjected to this. Was Cho telling the truth that she only ratted out the DA because she didn't want her mother to lose her job, or was Cho lying in order to cover her ass? Or, like Cho in the movie, was she finally forced to crack under the effects of Veritaserum?
When Sirius encouraged Harry to set up the DA, what was his main reason for doing so? Was it to make sure Harry and his friends could protect themselves against Voldemort, or was it the chance to rebel against The Man once again, through his godson?
Angst Dissonance: Harry's angst after Cedric's death and being left out of the fight against Voldemort by the Order (because the kid who saved their asses four times already can't possibly be useful), while justified, was still an annoyance to many readers.
It's likely that Harry has PTSD in this book. He watched a classmate die, was tortured, and forced to fight an older wizard with over 40 years and a lot of power on him. His angst is perfectly reasonable, but according to some doesn't make it any less obnoxious.
Subverted in the film, a rare instance where some prefer the film's portrayal to the book's. Harry's angst is downplayed to relative hesitation and uncertainty of himself as a leader. One little pep talk later and he gets over it.
Was Umbridge raped by the centaurs? If she was, did she deserve it?
And the matter that wracks many an entry in the Headscratchers page: was the Prophecy worth all this convoluted cloak-and-dagger stuff that forms much of Harry's angst throughout the book and ultimately got Sirius killed?
Designated Hero: Hermione Granger. First, there was jinxing the sign-up sheet for the DA to deform traitors without their knowledge. Then there was her complete inability to listen to reason when she kept trying to liberate the House Elves.
In fairness to the last one, just about every last character she talks to her about that disagrees with her, including Harry himself. Overall the narrative seems to paint her in the wrong.
In the film, Hermione also goes along with the blatant bullying of Luna Lovegood, introducing her as 'Loony' in the introductory scene of Luna to the others; for someone who has been bullied and subjected to abuse for her status at Hogwarts herself, you'd think Hermione would know better and would probably be more supportive and open-minded than others in terms of some of the things Luna comes out with. As it is, the film uses Luna's status to make her and Harry connect a little better, given they're both out on the fringes in terms of popularity at the beginning of the film.
Snape has a very sympathetic backstory, but Fandom sometimes will go out of its way to blame every one else and sugarcoat his part things that went wrong in his life.
Marietta as well to a smaller extent (since we know very little about her). The fandom often likes to imagine her as a tortured girl afraid of her mother losing her job at the Ministry - when there's very little evidence pointing to that in the book. Whatever her motivations, she still went to Umbridge of her own free will knowing people would be punished.
Freud Was Right: Dolores Umbridge's "avoidance and theoretics" approach to D.A.D.A as opposed to actual knowledge drew a lot of parallels to the U.S. sex ed debate. And that book was heavy handed as it was.
The Room of Requirement: a hidden area where teenagers sneak off to engage in "forbidden activities" and risk getting into deep trouble if caught.
"Funny Aneurysm" Moment: It's too easy to laugh at Neville's constant screw-ups, plus the fact that he lives with a near-tyrannical grandmother. But then in the fourth and fifth books, we learn exactly what happened to his mother and father, and how it has affected him. Then we feel guilty for having laughed.
Zacharias Smith's "I don't think Expelliarmus is exactly going to help us against You-Know-Who, do you?", given that this spell is what finally brings Voldemort down.
Harry says sarcastically to Malfoy, Crabbe and Goyle: "I'm terrified now. I suppose Lord Voldemort's just a warm-up act compared to you three?" In Deathly Hallows, those three are a warm-up act before the final confrontation with Voldy.
Regarting the Ordinary Wizardy Levels tests, there's one concerning the grades. The lowest grade possible is "Troll", presumably meaning that the student has the aptitude level of a regular in-universe troll. Time marched on and the concept of the Internet troll arose. This gives the grade a wholly different but still perfectly applicable explanation in that a student reaching that grade has got to be doing it on purpose to get a laugh at the examiners' expense, i.e. trolling them.
Idiot Plot: One reason why the book is such a Contested Sequel is that a lot of the main plot depends on people acting like total idiots and the plot and resolution feels highly contrived:
There is Harry himself who could have avoid lots of troubles and the ending altogether if he had 1) Listened to Dumbledore (and finished his Occlumency lessons), 2) Listened to Snape (and finished his Occlumency lessons), 3) Listened to Hermione, who despite not having a Scar-Hotline to Voldemort figured out that Harry was walking into a trap, and finally, 4) Simply listened to Sirius and used the mirror he gave him, and related to that, Sirius not mentioning the mirror to Harry when he contacted him through the fireplace.
There is Dumbledore who simply decided to keep Harry Locked Out of the Loop without even telling him basic details like don't take the scar visions too seriously (practical advice that needed no sharing of special secrets at all), who furthermore appointed Snape to give him the lessons despite knowing how he and Harry felt and not strong-arming Snape to be more patient with Harry. Related to this is the fact that, Occlumency ultimately plays no role in the final books and Dumbledore simply shrugs away the entire plot.
Likewise Dumbledore reveals that the Order has a secret means of communication that is inaccessible to the Death Eaters and later books reveal that it relates to the Patronus, apparently neither Dumbledore nor anyone in the Order felt it necessary for Harry to be able to contact them in an immediate, safe and accurate manner if he was in an emergency and needed to contact them. Especially since Harry knew how to cast a Patronus already.
Everything about Umbridge's assignment to Hogwarts. For starters, she's Obviously Evil, with her not-so-very subtle disdain for Harry during his trial, the fact that her name is apun on the word "umbrage", and her position allowing her access to the Dementors, you'd think Fudge would keep a sharper eye on her. Another problem is that Harry, or anybody else Umbridge punishes, doesn't just simply report her for her medieval disciplinary methods. Surely, Dumbledore would have believed Harry. While the scar the Black Quill leaves isn't noticeable, it's still there. How many children does Umbridge have to mutilate for somebody to get that she doesn't play for the right team? All of this was to demonstrate how ignorant Fudge was, but that's really going a long way just to give a commentary on politicians.
Cho for calling Hermione out on disfiguring her only friend and pointing out that she should have told the members of the DA that the sign-up sheet was jinxed.
Sirius is submitted to a lot of this in Harry Potter and the Order of the Phoenix with many characters mocking him for his "uselessness" to the Order while Hermione and Mrs. Weasley note how reckless he is. From what we see, Sirius was capable enough to be two years on the lam, disciplined enough to keep his sanity while imprisoned in Azkaban and his recklessness stems mostly from being cooped up in the house he hated and being submitted to Condescending Compassion from everyone around him, with Hermione expressing doubts about the advice of a full-fledged wizard. Indeed, had Harry listened to Sirius instead of Dumbledore or others, by using that Mirror he could have verified Sirius being safe and alive instead of charging at the Ministry. Dumbledore outright admits that Sirius was right for wanting to involve Harry on information with the Order.
Launcher of a Thousand Ships: Since this introduced some new characters, it also launched a few new ships. Most prominent was Harry/Luna and Neville/Luna.
Love to Hate: Few, if any, fictional characters are as supremely and utterly despicable as Dolores Umbridge.
Memetic Mutation: Umbridge's "I will have order!" She says it once in the movie and never in the book. Tellingly, by the time the next film was made, they saw fit to include an Umbridge doll in Weasleys' Wizard Wheezes which constantly squeals "I will have order!"
Memetic Psychopath: Between the jinxing of Marrietta and the popular theory that Umbridge was gang-raped by the centaurs with her having a victorious smile afterword, some fans like to think there's a sociopathic side to Hermione.
Moral Event Horizon: Dolores Jane Umbridge has long since passed over it. She starts by cheerfully calling Harry a liar, forcing him to cut into his own flesh and do lines with his own blood, tries to sabotage Gryffindor's chances of winning the Quidditch Cup by removing three of their best players, cruelly mocks Hagrid's teaching, gleefully tries to sack Professor Trelawney (and thoroughly enjoys her despondency), takes over from Dumbledore, tries to arrest Hagrid for no reason, nearly kills McGonagall in a sneak attack, and finally tries to used the Cruciatus Curse on Harry. Oh, and it turns out she was the one who set Dementors on Harry and Dudley in the beginning. So, take your pick. Oh, and guess what? She gets worse in Deathly Hallows.
In the movie, there's a scene that shows that she forces first years to use the Blood Quill.
UncleVernonDursley crosses it in the novel (but not in the film) when he tries to kick Harry out of the house, after finding that he would likely die in the hands of Lord Voldemort if he did this.
In his very slight defence, his reasoning for doing so are for the sake of his wife and son and their safety, not specifically because he wants to see Harry killed (though he wouldn't likely care if his nephew was killed). Vernon, not understanding magic and that he and Harry are both better off with Harry there, thinks he'd be protecting his family by getting rid of Harry.
What can't be defended, however, is that he very clearly wishes death upon Harry, as he all but outright stated earlier in that scene he hoped the Ministry of Magic executed him.
Narm: Some found Harry's meltdown in Dumbledore's office after Sirius died to be this. It looked less like he was venting his anger and more like one of Dudley's temper tantrums in the first book. The earlier rant in Grimmauld Place is like this too, with most of Harry's dialogue in block capitals - and some fans have jokingly nicknamed it 'Caps Lock Harry'.
Never Live It Down: The release of the fifth book and the "Snape's Worst Memory" chapter has become the defining image of James Potter's character among the book's fans and especially Snape's fans, rather than the positive way he was regarded and described in the first four books as a great wizard, loyal friend and good father. The fact that Rowling never bothered to flesh out James's life with more flashbacks showing him in a more positive light (after he "grew out of" his bully phase) doesn't help.
Nightmare Fuel: The Death Eater whose head — just his head — was regressed to infancy.
When those brain things attack Ron in the Department of Mysteries, shortly after Ron was struck by some curse that left him blabbering like a tiny child.
Umbridge. She sits in as a voting member of people's trials? She's allowed around children?! Her tactics are so draconian she may as well be a Death Eater. And Harry says so himself: "She's foul enough to be one."
And on the other side, her fate at hands of the centaurs. If you know anything about their traditional role in ancient mythology, it's quite clear that she was gang-raped by them.
The bureaucracy that is the Ministry Of Magic for turning a blind eye to the atrocities Umbridge committed. The Death Eaters had taken over the Ministry when Umbridge was at her very worst but this in no way excuses her actions.
Zacharias Smith of Hufflepuff is depicted very unsympathetically for merely asking why everybody is accepting Harry's story that Voldemort is back. Keep in mind that Harry's been described by the adult authorities as "disturbed and dangerous" and as an attention-seeking glory-hound. Also, Zach might have other reasons to distrust Harry—-Harry told a tabloid newspaper about Cedric Diggory's death first, instead of the boy's housemates, who idolized him and really wanted to know. For this high crime, Zach has become the fandom's Butt Monkey; very few characters get less sympathetic treatment than he does.
Marietta Edgecombe betrays the DA to Umbridge. This activates a secret jinx from Hermione that writes "SNEAK" across her face in boils. Cho considers this a mean trick, and eventually breaks up with Harry over it. Thing is, Marietta was motivated by the risk of her mother losing her job at the Ministry, never wanted to join in the first place (Cho pressured her), and it's kind of unethical to trick people into signing a contract that punishes them for betrayal without telling them. (Heck, Hermione didn't even let her best friends know what would happen until later.) Rowling herself seems to be firmly on Hermione's side; when she confirmed that Marietta was permanently scarred, she said "I loathe a traitor." The result: fans sympathize with Marietta more than the series main characters, much to Rowling's annoyance.
Becomes a case of Both Sides Have a Point: Harry during his last fight with Cho points out that Marietta also sold out Cho, her BEST FRIEND, for fear of Madam Edgecombe who was searching the school fires and loyally serving Umbridge, losing her job. Seriously. Marietta had six months to choose sides, and she was willing to let others get expelled, including Cho, for "family pressure". She also became an Unwitting Instigator of Doom because things go From Bad to Worse with Dumbledore forced on the lam and Umbridge taking over Hogwarts.
As for the jinx, there's a reason Hermione didn't tell anyone; if she told them, they could have set up a counter-jinx to nullify the contract's binding agreement. It also creates an aura of distrust if people are told that the contract they sign will expose them if they're disloyal.
Interestingly, Dolores Umbridge has the same opinion. She won't stand for disloyalty to the Minister for Magic, going to extremes (including physical abuse) to express this viewpoint. She permanently scars Harry with the words "I must not tell lies" on his hand. Food for thought.
The Ministry's claim that they need to interfere in Hogwarts in order to fix various problems with the way the school is run. They're doing it more for personal gain and paranoia about Dumbledore. However, the fact of the matter is that if a real school was run like Hogwarts (for example, letting a teacher bring dangerous animals to class), it probably would have been shut down.
They Just Didn't Care: In the film version the heated argument between Molly and Sirius over whether or not Harry is a true member of the Weasley family is played with about as much conviction as a soccer mom ordering McDonald's Happy Meals for her kids.
The scene of Snape's worst memory completely misses the point of why it was called that; not the bullying, but that he ruined his chances with Lily.
Though, in David Yates' defense for Snape's Worst Memory, the movie and Harry Potter and the Deathly Hallows were released around the same time, and Alan Rickman had to keep quiet about the fact that Snape was in love with Lily.
What an Idiot: Marietta attempting to rat out the DA, causing Dumbledore to leave could have easily been avoided if Hermione told the members that the sign-up sheet was jinxed, giving them another reason not to snitch.