When the characters were redesigned when the movie was retooled, the eye colors of Arlo and Spot were changed to match the other's primary color. Arlo has brown eyes, and Spot has green eyes.
Arlo's status as the runt of the litter actually saved him. When the flash flood hit him, he was swept away and had a lot of room to avoid debris and could swim to the centre. Poppa didn't have that; his size meant he would be more likely to hit something. It also let Arlo swim under some obstacles in the river as well. The end flood did not look wide/deep enough to allow an adult Apatosaurus to be fully submerged.
It's also possible that Poppa didn't know how to swim. Until he watched Spot and copied his movements, Arlo certainly didn't.
Thunderclap's group is a flock in two senses of the word: One is that it's a group of quasi-avian animals. The other is that it's a congregation of individuals who share a certain belief, i.e., their religious obsession with the storm.
If Thunderclap and his group's behavior are an indication, it can be said that their flock is, in all senses of the word, a cult.
Along similar lines, this makes Thunderclap's ultimate fate a case of Laser-Guided Karma. After preying on so many flood victims, he becomes one himself... with the help of a couple of his would-be meals.
Additionally, his beloved storm is what ultimately causes his downfall.
And if it is to be believed Thunderclap died, he's now nothing more than pickings for scavengers himself.
Thunderclap and Forest Woodbrush are two polar opposites of what Arlo could've been. On one hand, Forest is a benign version of Arlo if he allowed fear to control him. It's gotten to the point where Forest is a recluse who heavily relies on his 'pets' to "protect" him. Whereas Thunderclap is a malignant example of what would've happened to Arlo if he went with his resolve to not be afraid of anything ever again.
The raptors weren't depicted as evil simply because they were predators. The T. rexes were also predators. The raptors were evil because they were trying to steal from the T. rexes; the raptors are, for all intents and purposes, criminals.
The ultra-cartoony design of the dinosaurs in the very realistic environments is a questionable design choice... but take a look at the dinosaurs in the scene of the asteroid missing Earth. They look much more realistic than any character in the bulk of the film. Dinosaurs evolved into caricatures of themselves... just like in WALLE, when 700 years of living in space turned live-action humans into animated ones. Apparently, that's just how things work in the Pixar 'verse. Pixar logic!
It may seem odd that a T. rex would be threatened by something as (relatively) small as a crocodile. But then you remember that in the Mesozoic, some crocodilians reached — and even possibly slightly exceeded — the size of a full-grown Tyrannosaurus.
How is it that for all his wandering and absence from the farm, Arlo still gets his mark by the end of the story? Because his Poppa told him he'd earn his mark when he "took care of that critter". Given Spot is with a family who will keep him out of trouble (and out of the family silo), Arlo took good care of that critter.
Why wasn't Poppa bothered with Buck hitting Arlo's egg, and then loses his cool when Buck hits Arlo? Because before Arlo hatched, Poppa must've figured Arlo would be bigger than his brother, and therefore wouldn't be hurt by Buck's smacking. But upon seeing Arlo is smaller, Poppa is angered at seeing one of his kids bully their smaller sibling.
It might be hard to imagine a dangerous outlaw gang of Stegosaurus, as they are herbivorous dinosaurs. But Stegosaurus were probably one of the most dangerous dinosaurs of their time, not unlike certain herbivores today like rhinos and buffalos.
One thing this troper noticed: the longhorn bison the T. rexes keep appear to have wide feet with three toes, like a rhino instead of an actual buffalo, which has hooves. But if you think about the world of the film, this makes sense: because dinosaurs never went extinct, mammal evolution was pushed back several million years, and large ungulates haven't yet evolved the modern hoof shape, despite being recent species.
If you subscribe to The Pixar Theory, then eventually that means the film's cast is going to die off from something or other. Maybe even the Ice Age...
The story sets 65 million years after the Cretaceous and in the present day, so the Ice Age could have already ended. Besides there's plenty of evidence to suggest dinosaurs can perfectly thrive in cold climates.
Just because it's 65 million years after the Cretaceous, it does not mean that it can't take place a few thousand years before Brave (which is the next movie in the Pixar Theory timeline). In this movie there seem to be very few dinosaurs still alive, and they are struggling to survive (not being able to collect enough food for the winter is a major plot point), so it's quite possible that they eventually will go extinct and replaced by the descendants of Spot's species.
Initially, Butch doesn't really give Arlo much consideration and even threatens him a couple of times. Who's to say, when he told Arlo to "act as a distraction", he wasn't planning for the raptors to kill Arlo and Spot?
Even if Thunderclap survives the river and his wing heals, he'll be in for a nasty surprise when he realizes that the reason he nearly died is because his beloved storm swelled up the river...live by the sword, die by the sword.
Nothing is explicitly stated about how Spot's parents died, but there are clues that paint a disturbing picture: the culprits were none other than the Stormchasers. Sure, it might sound too simple, but look at the facts. One, Thunderclap and his cronies admitted to having eaten humans before; Coldfront catches Spot's scent and calls him "One of the juicy ones!" Two, Spot hid under the fallen tree as soon as he saw the Pterosaurs. Why would he do that? Because he knows from experience that they're dangerous. Three, the Stormchasers' behavior is atypical of Pterosaurs. If they all had a reputation for being ruthless and manipulative scavengers, Arlo wouldn't have called out to them for help. In conclusion... Spot watched his parents get picked apart by pterosaurs.
For most of the movie, Thunderclap and the Stormchasers largely go after "critters" and small animals. It would be easy to assume that they only go after hurt and helpless animals, and only went after Arlo because he was protecting Spot, until you realize that the very first thing Thunderclap said Arlo was asking whether or not he was injured - and once you know it's there, it's hard to miss the disappointment in his voice when he realizes Arlo isn't. It all adds up to a shocking realisation; they've killed and eaten other dinosaurs before.
Or, even worse, Spot's parent's were killed by Arlo's. Think about it. Spot would have had to have lived nearby for most of his life and, being as young as he is, wouldn't have wandered far and would have gone for the easiest food sources he knew of. Two young parents would have had to have known where to get extra food for a growing child, in an area with little obvious wild food. Papa, on the other hand, knew exactly how to capture and quickly kill critters like Spot. Almost like he had to do it a few times before...