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. Even in the movie, where the rhinoceros is a mass of black clouds and lightning and very possibly a metaphor for something else, it's pretty ridiculous.
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 led 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 its 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 have the same voice actor!
James begins his adventure by entering a fantastical ribbed tunnel to a strange house, at the climax, he has to run to safety as platforms are being torn away beneath his feet, and he defiantly shouts "no, I'm not!" in the final confrontation. All of these are also experiences that the eponymous heroine of a later Selick film will have.
Not to mention finding a mother figure in a spider-like creature. Thankfully, Miss Spider is actually benevolent.
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)!
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.
They Wasted a Perfectly Good Plot: The concept of turning the ordinary rhino that killed James' parents in the book into a Chernabog-esque Eldritch 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?
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.
Taken Up to Eleven in the musical. We first see James in an orphanage having a nightmare about his parents' deaths. Then, the Matron Nurse tells him he's leaving the orphanage to go live with his aunts, whom he's never met while telling him not to be a nuisance because he can't ever go back to the orphanage. Spiker and Sponge take every opportunity to taunt James AND his deceased parents, call him worthless and threaten to put him down a well as punishment. To top it off, they destroy James's mother's scarf and his father's glasses IN FRONT OF HIM while telling him he has to sleep outside. And the best part? He's between the ages of six and eight (like the book), as the musical confirms James is young enough to still be afraid of the dark. By the time James has his second nightmare on the peach and tells the insects that his parents are dead, he's pretty much on the verge of an emotional breakdown. Thank goodness "Everywhere That You Are" starts up.
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 Jerkass 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.