Adaptation Expansion: Based very loosely on a children’s book by Hudson Talbot. Half of the dinosaur characters are dropped with more human characters added as well as an antagonist and loads and loads of side-plots.
If for no other reason than the implication that dinosaurs aren't appealing to kids unless they're turned into cuddly goofballs.
Small potatoes in comparison, but pterosaurs aren't freakin' dinosaurs. It doesn't help that Elsa looks nothing like a pteranodon.
Woog and Dweeb, a Triceratops and Parasaurolophus respectively, are both seen eating hotdogs.
Then again, Triceratops might had been an omnivore, and herbivorous animals do occasionally eat meat (although having a diet like Woog's and Dweeb's would certainly be unhealthy).
Rex has three functional fingers in each hand, despite T-Rex having only two in real life.
Baleful Polymorph: This happens to Louie and Cecilia when Professor Screweyes, having put them under his spell with his screw eye, demonstrates the power of his evil pills to the dinosaurs by giving one to the kids, turning them into monkeys.
There are some deeply Unfortunate Implications here. Professor Neweyes tells us that Brain Grain has essentially caused world peace in his home time, since living things that eat it will no longer harm each other at all. Given that Brain Grain also turns Rex into what amounts to a Barney rip-off, and without it, he's a vicious slavering murderbeast... well, see What Measure Is a Non-Cute? below.
Character Customization: When the movie first came out, Louie used to have some of his teeth missing and Cecilia's hair color used to be dirty blond with a red tint.
But then the upcoming direct-to-DVD reissue of the movie decides to have Louie's mouth being edited to show his teeth in its entirety and Cecilia's hair color being changed to just dirty blond without any tint or color mixed in.
This was actually explained pretty well in a highly rated youtube comment on the scene: "In a deleted scene he goes into great detail about how his worst fear is crows, and that's why he uses them in his act. This way, the crows are under his control. Also, his job at the circus is to frighten other people, showing how he even controls fear itself! But then, the circus is shut down. The people leave. Even the acts leave, excluding the crows. Suddenly, he realizes he is just a lonely and frightened man, with no real control, and he is consumed by his own fears."
Deus ex Machina: Convenient timing helps when you have an actual Time Machine. But then again, couldn't he have arrived before the heroes got trapped in the evil circus?
Devolution Device: Screweyes' Brain Drain pills, which he uses to briefly transform the kids into chimpanzees and revert the dinosaurs to their pre-Brain Grain forms. Which are violent and monstrous. Huh.
The Dog Bites Back: The crows who are present whenever Prof. Screweyes appears in the movie circus seems to dislike him for some reason: so when he's left alone they took the chance to eat him alive.
Eye Scream: In the cut scene where Prof. Screweyes explains why he became a villain he tells in disturbing detail of how a berry fell into his left eye and a hungry crow pecked the eye out when trying to obtain it.
Evil Twin: Actually, just an ordinary brother, not a twin brother.
They never mentioned if they were twins or not... they certainly looked a lot alike, if you leave the screw eye and all that aside...
Everything's Better with Dinosaurs: According to most of the kids, it would be. On the other hand, the fact that some kids and virtually all adults are scared by the idea of actual dinosaurs running about is why Screweyes wants to get his hands on the heroes. That said, when he does get his hands on the protagonists and turns them mean with his evil pills, they don't rampage so much as sit there and look angry.
Only because they're chained, though... one can only imagine what would have happened if they had escaped the circus...
Hellish Pupils: The slot in Screweyes' screw-eye is positioned vertically to give it this effect, and is sometimes shown as being elliptical like a cat's eye. It even moves in his socket like a normal eye would just before the crows attack him.
Hypnotic Eyes: Professor Screweyes' screw eye. It is able to hypnotize people (*cough*), despite the fact that it's only a screw thrust in his eyesocket. The backstory of the "eye" is what makes everything so disturbing; take a look at Eye Scream above.
Informed Ability: Much of Neweyes' plan (and the film's plot) hinges on the dinosaurs' apparent intelligence and abilities — to navigate New York City, to handle the modern world, to make up their own minds about what they want to do with their lives. In reality, they're extremely childlike and naive, and this nearly winds up being their undoing.
Interspecies Romance: Elsa is very straightforward about her crush on Rex, much to his initial discomfort. Whether or not he returns her feelings in the end is sort of hard to tell.
Jerkass Has a Point: Screweyes has an agreement with Stubbs the clown — if Stubbs can make him laugh, he'll put his act in the show. And while this is indeed leading the poor guy on, the fact still remains that Screweyes' circus is not a goofy clown kind of circus in any way, shape, or form.
Knight of Cerebus: After Screweyes and his Circus Of Fear shows up the movie takes on a decidedly darker turn. The villain is genuinely charismatic and the goofy dinosaurs are no longer funny, even before he turns them monstrous. While it is in no way an appropriate direction for this silly kid's film to take, for older viewers who are into weird animation, it's the best part of the movie — but it is also short (even shorter without the deleted scenes).
My Beloved Smother: Louie claims his mother is this trope as his reason for running away, but to hear him describe it, it sounds more like he's just massively insecure in his own masculinity.
Never Trust a Trailer: The trailer gave the impression that Screweye's role as the "Master of Fear" would have been more prominent and that the dinosaurs only appeared monstrous during his act as the result of his machine. Screweyes is only in the movie during the last 25 minutes or so and is more of a pathetic, ineffectual villain, and the dinosaurs actually turned evil as the result of his pills.
Parental Abandonment: Cecilia's parents are never around, and don't even take her on vacation with them. In contrast, Louie is the one abandoning his parents, as apparently he was embarrassed of his mother showering him with affection at every opportunity.
What Measure Is a Non-Cute?: And it is wikkid Anvilicious about this too. The dinosaurs are turned into BarneyExpies when they're "tamed". Once Professor Screweyes gets a hold of them, they turn ferocious and terrifying... but Rex's "normal" form in the beginning is ridiculously monstrous already.
Let's not even get into the irony that comes from the fact that when they become intelligent, they wind up looking, well, really dumb. In their feral forms, they look more clever and respectable than they do as Happy Meal toys. Huh?
What Happened to the Mouse?: When the group is boarding the ship to leave Screweyes' circus, Neweyes says that he has a surprise for them. Unless he was referring to the five minute ride to the museum, we never do learn what the surprise was.