In the line of the previous, Rowling originally intended for the book to include more Foreshadowing and other things like that related to the main plot of the series, but her editor deemed these parts unnecessary and ordered her to remove them. Since this was only her second book, Rowling had yet to obtain her Auteur License and had to comply. Most of what she wanted to reveal in this book ended up getting moved to Half-Blood Prince, resulting in Chamber Of Secrets getting criticized for not doing much to advance the Myth Arc of the series and Half-Blood Prince for being rather Exposition heavy.
Early on, the entire storyline about Harry finding the Half-Blood Prince's textbook was intended to happen in this book, alongside the storyline about the Chamber of Secrets. In fact, Harry Potter and the Half-Blood Prince was this book's Working Title. Rowling decided on her own that the two storylines didn't mesh and therefore determined that the Half-Blood Prince storyline would be saved for a later book.
Rowling had written a chapter named "Malfoy and Nott" that was a meeting between said characters. In it, Nott came with his son to Malfoy Manor to discuss with Lucius whatever Death Eaters discuss, with Draco and Theodore having one of their own in the garden about Dumbledore, Harry and the stories the Death Eaters tell about The Boy Who Lived. Rowling said that it would have been a look at Draco actually seeing someone as his equal, because they were just as good students as each other and come from just as "elite" families. She especially liked this chapter, but was forced to cut it from the book because it felt out of place (most probably following her editor's orders). Rowling later tried to work it in in the fourth book, but it was cut as well and she gave up on it.
Nearly Headless Nick's backstory was originally going to be described in a rhyme.
Penelope Clearwater was a fifth year in early printings, making her a year younger than Percy. Later printings changed her to a sixth year.
In an earlier draft, Harry and Ron crashed the Ford Angelia into the lake, where they were rescued by the merpeople. At the time, Rowling imagined that the merpeople would play a big role in later books and therefore needed to be set up early on. However, because they played no more part in the plot of this book, her editor objected to the scene, decreeing that they were a Wacky Wayside Tribe. Ultimately, they were replaced with the Whomping Willow, which is relevant to the very next book, and the merpeople never became as important in later books as Rowling thought they might.
Film
Casting
Madam Hooch was slated to return, but Zoë Wanamaker didn't like the salary she was being offered and turned it down. All of Madam Hooch's lines were then given to McGonagall.
Alan Cumming was offered the part of Gilderoy Lockhart, but turned it down upon hearing that Rupert Grint and Emma Watson would be making more money than him on the project.
Warner Bros had Hugh Grant as their first choice to play Gilderoy Lockhart. Grant accepted the role, but scheduling conflicts with Two Weeks Notice forced him to step away. Had he played Lockhart, it would have been his second time working with Chris Columbus, who had directed him in Nine Months.
Jason Isaacs initially read for Lockhart, but Chris Columbus asked if he could read for Lucius Malfoy. Isaacs was hesitant, as he was already signed up for a children's literature villain as Captain Hook in Peter Pan, but eventually embraced the role as his own.
The initial concept for Lucius Malfoy was of a man with Isaacs' short dark hair and a pinstriped suit. However, when they showed it to Isaacs, he argued that Lucius, being a wizard supremacist, would want to look as different from a Muggle as possible. He suggested a long blond wig, a velvet cloak and a cane for grand gestures, leading to the iconic Lucius Malfoy look. Isaacs also had the idea to give Lucius his signature icy voice, inspired by a former drama teacher of his, although Columbus initially didn't like this and it was Daniel Radcliffe who convinced him that it would work.
Richard E. Grant and Bill Nighy (who eventually played Rufus Scrimgeour) were considered for the role of Lucius.
Oddly enough, the two leads from Fantastic Beasts, Eddie Redmayne and Jude Law, auditioned for the roles in this movie. Redmayne auditioned for Tom Riddle but admitted he botched it and Christian Coulson was cast. He would later be cast as protagonist Newt Scamander in 2015 for the first installment, Fantastic Beasts and Where to Find Them. Law was almost cast as Lockhart but the producers thought he looked too young. He'd go on to be cast as Albus Dumbledore in 2017 for the series's second installment, Fantastic Beasts: The Crimes of Grindelwald.
Other
Although Chris Columbus returned to direct, Frank Oz said in an interview with The A.V. Club that he was asked to direct this movie, but he had no interest in it.
In the early stages of production on the film, concept art was drawn for the Deathday Party scene.
The area at the top of Dumbledore's office contains a weird telescope, which you can see up close in the DVD tour feature. In a DVD documentary, Chris Columbus explains that they may want to use the telescope in "the third or fourth film", which obviously didn't happen, due to the switch in directors. Ultimately, the telescope area wouldn't be seen up close in the films until the Snape's memories scene in Deathly Hallows, Part 2.
The original script contained the scene where Hermione gets a get well soon card from Lockhart, as well as a scene where Ginny sees Harry with the diary.
Released behind-the-scenes footage shows the filming of a scene in which the trio are gathered around a table in the Gryffindor common room as they discuss McGonagall's lecture on the Chamber of Secrets. The final cut features the exact same dialogue, but it's been moved to a Walk and Talk scene in a Hogwarts corridor.
