Crosses the Line Twice: In true Roald Dahl fashion, James' parents abruptly getting eaten by a rhinoceros at the beginning of the story is so deliberately absurd that it's near-impossible to find it all that tragic.
Family-Unfriendly Aesop: Don't like your own lot in life? Want a better quality of life? Become an illegal immigrant, according to James and friends.
The undead pirate scene, which is lead by Jack Skellington, has an expy of Donald Duck among his crew. Six years later, Kingdom Hearts was released, with Donald as one of the main characters and Halloween Town being a playable world, with Jack serving as it's Guest-Star Party Member. Likewise, the main party become undead there, though Donald is turned into a Mummy instead. Even more hilarious in the French dub of the film; Sora and James share a voice actor!
Ho Yay: A private violin performance of Bach's Partita No. 3, Gavotte en Rondeau, as their mode of transport soars over a moonlit sea seems to edge on the romantic side of things; especially when one considers how flustered Mr. Grasshopper is to be caught by James in the middle of things.
Moral Event Horizon: Both Aunt Sponge and Aunt Spiker are abusive legal guardians towards James in the movie. However, they finally cross it when they outright attempt to MURDER him with axes (with all of New York City watching, no less)!
Narm: James has a very thick accent that causes him to replace some of his "r"s with "w" sounds. For American viewers, this can make him sound like a very young child and give his lines a certain level of Narm.
A few of the special effects are quite unconvincing, such as the clearly wooden seagull puppets, the clearly cgi-mechanical shark and ocean water, and the clearly painted backdrops used for NYC.
James. Poor, poor James. He had such Good Parents, until they died and his evil aunts took him in. You can guess how well THAT went for him. Worse, while watching his aunts publicize the giant peach, kids are present there. However, James is forbidden to leave the house, and he sheds a tear as the only possible friends he would make just come and go.
Miss Spider can also come across as this in the book. It's hard to not feel bad for her when she confesses that she doesn't understand why people hate spiders, or when she bursts into tears in the middle of talking about her relatives being killed in front of her. Her film counterpart, while more of a Deadpan Snarker, also has some shades of woobiness as well; she isolates herself because she's aware the other bugs fear and distrust her, and she admits that she doesn't know what it's like to have friends.
Mr. Centipede, at least in the movie, could be seen as a Jerk Ass Woobie if you read his boisterous attitude as mostly bravado; it's hard not to feel for him after he accidentally steers the ship off-course and the other bugs shun him.
They Wasted a Perfectly Good Plot: The concept of turning the ordinary rhino that killed James' parents in the book into a Chernabog-esque Eldrich abomination itself was not a bad idea and could have worked perfectly.The trouble was that the writers were far too lazy with executing it, not giving it any backstory or apparent motive, making the concept confusing. Why did it attack James parents in the first place? Were the aunts aware that it was a cloud monster in the beginning, or just taunting him? Why did the rhino wait until the group reached New York to attack them as opposed to earlier? Was it even real or just James imagination?
Here's how it could have worked in the movie: the rhino was an eldritch abomination that the old man was put in charge of locking up. But it escaped one night due to his carelessness, and when it entered earth, it killed James parents merely because they were the first people it saw, but not James because it did not notice him. There also could have been a subplot about the authorities not believing James about the rhino's true self and assuming that the shock of seeing an ordinary rhino eat his parents traumatized him so much that he imaged the rhino that way. It also would have explained why the old man wanted to help James escape, since HE was indirectly responsible for his parents death.