Why does the female Velociraptor think Amanda Kirby had the eggs? The pack itself. It was mostly composed of males and the female confronting the group, presumably the mother of the eggs, was clearly barking orders to them and wielded enough power one hiss by her caused a male to stop in his tracks when he tried to charge. Possibly the pack follows a similar pecking order to spotted hyena clans and are matriarchal. So when the presumably alpha female confronted Mrs. Kirby, she did so because she could tell that Amanda was the only female in the human "pack" and assumed Amanda was their leader.
Compared to everyone else present, Amanda is the most brightly dressed (pink shirt and white pants). If the matriarch did not recognize Amanda as a female by, say, scent, it may have assumed Amanda's gender based on the coloration of her clothes as she herself can be distinguished by her bright white skin pigment compared to her darker male subordinates.
The Velociraptors being less vicious and more intelligent than in the previous films makes a lot of sense when you remember these raptors have been raised in the wild. The previous ones were raised in captivity (and in the case of Lost World, just recently freed), and therefore didn’t have as much experience with pack hunting.
Why is the Spinosaurus so much larger and more powerful than it should be (to the point of defeating a Tyrannosaurus rex)? Jurassic World provides an answer: it was an early version of the super-enhanced Indominus rex.
The movie's logo shows all three members of the Big Bad Ensemble: The skeleton of the Spinosaurus, the claw marks left by the Velociraptors (which also make the III in the logo) and two Pteranodons below the title.
It's lucky for the Kirbys that the three mercenaries didn't survive the trip to get paid. The Kirbys would have been several kinds of screwed if the mercenaries found out that they had been stiffed on their bill. At best, the mercs might sic collections agencies on them. At worst, they might abandon the Kirbys on Isla Sorna or just outright rob and kill them to collect what was owed.
Killing the Kirbys is something they wouldn't do, no way in hell.
They're only contractors. They're not even criminals. A shady bunch, maybe, and they might be willing to break the law if they get away with it. But none of them, least Udesky, is a killer. If they were they wouldn't have worked for the Kirbys but offed them right away.
The U.S. Navy and Marines coming to the rescue of the survivors at the end looks awesome, but considering the circumstances it's downright sinister. The Kirbys admit that they already tried to approach the government to send a rescue team and were told to just let their son die. Then Ellie uses her husband's connections in the State Department and suddenly it's not a problem?
The Kirbys went to the embassy after some time had passed (Amanda wasn't on the boat, or she'd be dead too, so we don't know how immediately she found out Ben and Eric were missing) and said "Two people with absolutely no survival training have been lost on Forbidden Dinosaur Island." Even Grant assumes Ben and Eric are a lost cause when he learns about it. The Kirbys basically asked the government to mobilize and invade another country's restricted territory to retrieve whatever's left of two corpses, assuming they could even convince whoever they talked to that they weren't a couple of delusional pranksters. Ellie and her husband are much more credible, and Ellie had contact with Grant thirty seconds ago and knows he's in immediate danger.
