The Spinosaurus being able to snap a T. rex's neck; the third movie's "dinosaur consultant" went on record claiming this was actually possible. In reality, a Spinosaurus's jaws were too weak to do so and their hands and arms were anatomically incapable of holding on to the T. rex in the manner it does.
Not to mention, T. rex had one of the thickest necks of all predatory dinosaurs, which some scientists speculate it used to pick up medium sized dinosaurs and shake them to death in its jaws, whereas Spinosaurus had a long, thin neck to allow it to move its head quickly into the water to catch fish using its long, narrow jaws. It would be like trying to get a pelican to try to snap a bulldog's neck. Also, the T. Rex had one of the strongest sets of jaws, proportionally, of all creatures to ever exist. The Spinosaurus wouldn't have been able to survive one bite to the neck. Sure, maybe the T. Rex was off its game or something...
Just for grins, after the movie shooting was done, the effects team pitted the "Spinosaurus" animatron against the "T-Rex" animatron; the T-rex won handily.
Lampshaded by Dr. Grant's remarks at his lecture at the beginning of the movie: he does not consider the Jurassic Park creatures true dinosaurs, but rather genetically engineered monsters. This is shown again by the completely impossible behavior of the Pteranodons. The actual inaccuracies and accuracies in the pterosaurs of the movie are too numerous to list here but anyone who would like to actually look it up can read the Stock Dinosaurs (Non-Dinosaurs) page, which has a whole folder dedicated to describing pterosaurs.
To be frank, the whole 'Spino breaking a Rex's neck' thing is only so hated because T. rex lost, not just because of its scientific innacuracy. There are many more far more drastic bullshit in Jurassic Park- T. rex having a prehensile tongue, poison-spitting Dilophosaurs, eucaptylus chewing sauropods, 10 foot Velociraptors, Dilophosaurus being the size of turkeys....frankly, messing around with purely hypothetical strength levels is the least of JP's paleontological problems, and if one is truly worried about accuracy there are plenty more stuff one should be annoyed about.
Refitted For Sequel: Many scenes in the film are from the books: The river chase and aviary from the first and the cloning lab from The Lost World. It's been joked that III exists mainly to use up all the bits from the books they couldn't fit into the first two movies.
The incorrectness of the Jurassic Park Dinosaurs is Handwaved and Justified by Grant in that these dinosaurs are mutants, not real dinosaurs (thanks to having their DNA spliced by frog DNA.) One of the changes includes putting some feathers on the head of the raptors.
Around the time this film was made, it was not yet known that pterosaurs didn't rear their young like birds.
Dr. Malcolm was in the original script, but Jeff Goldblum had to drop out.
A Baryonyx◊ had Spinosaurus' role in the original script. This was referenced in-movie. Billy guesses the dinosaur that attacked the plane is a Baryonyx, but Grant corrects him, saying Baryonyx didn't have that impressive sail on the back.
The ending was changed a lot; in the original script, the Spinosaurus was attacked by raptors and killed at the end; this was probably changed because in the first movie, the raptors were no match for the T. rex, and having them bring down an even bigger carnivore that actually killed a T. rex earlier in the film wouldn't seem realistic. note To be fair, the T. rex only fought one raptor, having killed the second one by surprise. Also, the helicopter was to be attacked by Pteranodons. And they also considered to have the Spinosaurus attack the marines.