Ass Pull: The plot twists about Jean Claude being Quasimodo's brother and Quasimodo being handsome were very forced.
Broken Aesop: The movie is supposed to teach that True Beauty Is on the Inside, but Quasimodo became beautiful, so the moral is: looks don't matter as long as you're handsome. Not helping by the fact that Quasimodo doesn't even look grotesque in the first place and that Quasimodo barely gets to do anything noble or heroic — besides saving Melody from being executed by Jean Claude right at the end, mostly by ironically enough, not doing something — during the whole film.
Creator's Pet: Melody's instruments are hated because of their jokes, useless dialog and overtaking on the film. This article discusses it. Despite this, they are a Spotlight-Stealing Squad, getting more screentime than Quasimodo or Melody. All the good characters in the film like them.
Epileptic Trees: Pierre is theorized to not really be Pierre Gringoire, but instead an original character given a stereotypically French name that happens to match the character name from the book.
Though not a fan in the slightest, Phelous has made the names "Inane Banter Squad" (the instruments) and "The Day-Dimension Bats" popular with viewers.
Glurge: This story was transformed into an uplifting story of a man who learned to stand up to himself, except it implied that ugly or deformed people are just shy people and that sadness made them like that.
Hollywood Homely: Quasimodo is or was supposed to be ugly, but he is not ugly at all. He just has an emo hairstyle and slouches.
Older Than They Think: Oddly enough, this wasn't the first screen version of The Hunchback of Notre Dame in which Quasimodo is handsome and it ends with Esmeralda marrying him - the now-lost silent film The Darling of Paris did it almost 80 years earlier.
The song when Melody is imprisoned and the last song do not advance the "plot" at all.
The scenes where the instruments climb the stairs.
Phelous: Will they make it up these stairs? Will you give a shit?!
Melody's mother getting all of the instruments in the barn when her daughter comes to rescue her. This leads to Melody getting captured by Jean Claude.
Rooting for the Empire: Jean Claude. Even if he's a Gaston ripoff, he's about the only tolerable character in the movie.
The scene of some gypsies dancing near a fire pit and Melody shaking her arms is repeated several times, even when that scene doesn't fit (including in the middle of the climax), which worsens the already present confusion between day and night.
A similar problem always happens with the bats. No matter where the characters are or what time of day it is, the bats are always shown in the same area in the daytime. Even when they open the door for Melody and her instruments or when they talk to Quasimodo when he is nowhere near their location.
Strangled by the Red String: Quasimodo and Melody have barely known themselves and then they're singing a song about love, imagining their wedding and even more, they get married a few days after having known each other.
They Changed It, Now It Sucks!: Even moreso than other derivative works from Victor Hugo, since the plot is barely recognizable as "The Hunchback of Notre Dame", Quasimodo is not ugly nor a hunchback at all and the ending is too happy for a film based on a tragedy. If the Disney version has some detractors for being a Disneyfication despite having themes too dark for a children's movie, Victor Hugo's fans were less than pleased with this film.
The Un-Twist: Pierre reveals pretty early on in the movie that Quasimodo and Jean Claude are half-brothers. The climax of the movie reveals the same thing, but with less exposition and is done as a "The Reason You Suck" Speech.
Despite this, they are a Spotlight-Stealing Squad, getting more screentime than Quasimodo or Melody. All the good characters in the film like them.