The death of Udesky, who is horribly used as living bait by the Velociraptors. They pretty much paralyze him (but don't kill him... yet), wait for one of the other humans to try and help him, and spring out when Amanda does. However, the humans escape, and the raptors leave... but not before one of them snaps Udesky's neck, putting him out of his misery.
Unlike its predecessors, the third movie's velociraptors are a lot smarter, can communicate, are better parents, and are willing to work together to bring down their prey...Their targets mainly being the protagonists.
The Spinosaurus: it killed the T. rex with ease and is very persistent, chasing the protagonists across most of the island and surviving being rammed by a plane.
The sound of the phone is still ringing in the Spinosaurus' belly... It could give one chills, when it's discovered standing behind them when they realized their mistake
The whole plane scene when the Spinosaurous is introduced.
Billy has a machine build the resonating chamber of a raptor, and blows into it to demonstrate. The look on Grant's face is priceless; it's clear that he has nightmares about that sound and it's enough to make your teeth curl.
Such a thing is even discussed in an earlier scene, where Grant talks his new theory over with Ellie.
Grant: Do you remember the noises they made? Ellie: I try not to.
When they trap one raptor in the facility, it starts making a panicked, but consistent noise. Grant has a major Oh Crap moment, as he realizes his theory about raptor intelligence was on the money.
"It's calling for help."
The whole scene with the Pteranodons. The introduction was specially frightening. First, Paul crosses the foggy bridge before his son does and, once on the other side, calls for his son to cross over. Once Eric goes, Grant soon realizes that they're all in a "bird cage." Cue Eric alone on the foggy bridge as an ominous, tall, inhuman like shadow appears in front of him. Then the screaming starts...
Then we're led to believe that Billy was killed after being stabbed and pecked at by a pair of pteranodons. The next scene then shows a terrified Grant looking into the glaring eyes of a third pteranodon before running away.
Eric was almost eaten alive by a large group of pteranodonbabies. All while on top of a small cliff.