In the film, when Harry jumps through the wall of fire to pursue Bellatrix, Lupin is the first of the adults to run forward. Is he concerned for Harry's safety, or is he going after the woman who killed his best friend? Probably both.
Minor one but Hermione's crying after Ron kisses Lavender. Some found it Narm, while others had a She Really Can Act reaction towards Emma Watson.
Lavender being played by a white actress was another one, mostly since she'd been entirely in the background with no lines in the previous films. Some felt it was pointless to change her back to white, while others felt it was more in line with the booknote When Ron and Lavender are making out, Harry mentions that it's hard to tell whose hands were whose, implying Lavender to be white. A third camp felt the Race Lift was necessary to avoid Unfortunate Implications - since that would have made both Harry and Ron's Romantic False Leads ethnic while their canon partners were white.
Big Lipped Alligator Moment: The Burrow-burning and Bellatrix's appearance in The Movie; Word Of God says The Burrow attack was to bring the threat of the Death Eaters more close to home to the characters than Hermione reading about it in the papers, but it still arrives and leaves without another word in true BLAM fashion.
Broken Base: The book that ignited the greatest quantity of flame wars on forums. Especially over the Ship Sinking.
Captain Obvious Reveal: Snape being the Half-Blood Prince surprised nobody. The first clue was Snape getting promoted to Defense Against the Dark Arts teacher, which is a dead giveaway that a character is going to be important in a Harry Potter book. The second, more glaring hint was that the HBP was good at potions.
Designated Villain: Cormac. He may be a jerk, but he suffers through a lot of Disproportionate Retribution, like having his Quidditch try-out rigged or having a month of detention for accidentally vomiting on Snape. Though, in the book, he's even worse and Hermione is called out on rigging his tryouts by Harry.
Double Standard: Abuse, Female on Male: To say the least of the infamous bird attack scene. Many a Ron the Death Eater fanfics will have Ron attack Hermione in a fit of jealousy. Hermione attacks Ron, in canon, and it is for the most part swept under the rug. note While both sides are portrayed as being petty, Hermione is still never called out on for resorting to violence. The film at least softens this, so that Ron isn't actually hurt with the birds like he is in the books.
Draco in Leather Pants: Hey Draco, that's a nice suit you got there. Of course, it helps that Draco starts to become a lot more pitiable by the end of the book, what with it being revealed that he's terrified of dying and/or causing the death of his family.
Fan Nickname: Disappointment in the movie caused some fans to nickname it "Harry Potter and the Half-Baked Script".
Foe Yay: Thank God Harry's obvious obsession with Draco was eaten by the giant chest monster, who decided to save the appearances just in time. Note that the word 'obsessed' is used in-story by both the narrator and a rather-concerned Ron.
Also Harsher in Hindsight: Dumbledore's "Oh, to be young and to feel love's keen sting" line in the infirmary upon Lavender hearing a bedridden, unconscious Ron call out to Hermione. In the backstory provided by Rowling, Dumbledore was in love with Grindelwald, who left the country after a fight Grinedlwald had with Dumbledore's brother led to the death of their sister. It was also Dumbledore who had to put an end to Gregorovich's reign of terror.
Hilarious in Hindsight: In the first book, Ron sees in the Mirror of Erised himself as Head Boy and holding the Quidditch Cup. He manages both (almost, as he became a Prefect) in this book and film. Also a little harsh considering that Ron never attends his last year at Hogwarts, meaning that there's a chance that he could have qualified for Head Boy but still couldn't take the position.
Outside of the Ship-to-Ship Combat, words can not describe the level of backlash fangirls displayed when Blaise Zabini was revealed to be, wait for it, black. Which was followed by "Wait, Blaise is a DUDE!?" Pretty much making thousands of Female Blaise fics void (or just a different genre now).
There were also a lot of complaints from non-shippers who were bothered by the book's focus on romance. Probably at least in part a Hype Backlash due to the massive focus those subplots got in the eyes of the rest of the fandom, but even so, it's a little unreasonable that they expected a book about 16-year-olds at a boarding school not to discuss dating and romance.
Jerkass Woobie: Morfin Gaunt. While he is established to be a fairly nasty wizard, it becomes hard not to feel sorry for him after he loses his father to Azkaban and Voldemort frames him for three of the murders he committed. Dumbledore himself lampshades it.
Similarly, "SNAPE KILLS DUMBLEDORE ON PAGE 606/596." (page 606 is commonly used as it has Harry explicitly saying "Snape killed Dumbledore," but the actual death occurs on 596. Or 566/556, depending on which edition you're reading.)
Amusingly, someone changed the Wikipedia page for the book to spoiler the ending. The IP address traced back to the HQ of the Minnesota Republican Party.
Harry reveals in-universe that he believed that Cornelius Fudge crossed it by setting Umbridge on the school in Order of the Phoenix. He is outraged when Dumbledore tells him that Fudge wanted Harry to serve as a pep coach for the wizardry public, giving Rufus Scrimgoer the idea, and Harry cannot believe that Fudge would think Harry would forget all the things Umbridge did.
Draco nearly crosses it when he tries to use the Cruciatus Curse on Harry in the bathroom. Subverted when he tries to kill Dumbledore because he doesn't have the nerve to do it and is only trying out of fear of Voldemort killing him or his parents.
Poor, poor Ginny. There's no evidence that she goes further than kissing with anyone, and with a grand total of two boys before Harry, and yet the bashers are all too happy to label her the "Hogwarts whore". Especially amusing as Ginny has to put up with the same accusations from her brothers in the very same book. She swiftly shuts them up.
Draco's No-Holds-Barred Beatdown of Harry on the train. Amazingly no one ever brings up Harry almost killing Draco later in the story.
Romantic Plot Tumor: Thankfully avoided. Although the book takes a greater focus on adolescent romantic histrionics than the others in the series, it doesn't dominate the main plot.
This was the film's main problem. The screenplay excised or downplayed many of Harry and Dumbledore's adventures into Voldemort's past (the A plot) in favor of Harry's teenage woes (the B plot).
Ship-to-Ship Combat: This book caused the shipping wars in the fandom to go nuclear, to the point of Emerson, the founder of Mugglenet, accusing some shippers of Fan Dumb in an interview. J.K. Rowling's reaction to this was akin to "Oh shit. Did you just say that? Do you want the rabid shippers to slit your throat in your sleep?" and she refused to call "a significant part of my fanbase 'deluded'". In spite of her refusal, angry fans made it seem like she had personally insulted them and spat into their faces.
Lupin and Tonks. In Half-Blood Prince, Harry sees Tonks upset several times and thinks it's over Sirius dying, and that maybe she was even in love with him. Then the climax reveals that Tonks is deeply in love with and wants to marry Lupin. They proceed to do so despite having no interaction on camera before this (although eagle eyed readers will notice that they tend to work together a lot in Order of the Phoenix). As the books are primarily written from Harry's perspective, it's somewhat understandable that plenty of major events can happen off-camera simply because Harry can't be present for every single storyline. At the same time, the reader can still feel left out as the key parts of the Romance Arc never actually happen in front of them either.
Unintentionally Unsympathetic: Hermione during her feud with Ron. While what Ron did may have been a low blow, Hermione reacts to it with complete immaturity by assaulting Ron with birds. Her inability to take the high road was only Hand Waved, as mentioned in the Double Standard: Abuse, Female on Male entry. Harry likewise seems to lose any sympathy for her when she invites Cormac MacLaggen to the Christmas party, solely to annoy Ron.