Nick Van Owen:[awkwardly, gesturing between the reunited father and daughter] Do you see any family resemblance here?
What really sells it is Eddie giving an "a little bit" gesture in response.
When the Tyrannosaurus is rampaging through San Diego: while chasing Malcolm and Harding in their car, San Diego police and Animal Control show up. They have just enough time to get one good look at the T. rex before it roars and they throw their cars into reverse.
Just the fact that an Animal Control vehicle is there, too. Yeah, dinosaurs are animals, too, but you kinda have to wonder if they were thinking "So What Do We Do Now??"
Also in that sequence, Ian and Sarah are trying to get the T. rex's attention so they can lead it back to the boat.
Ian: It's never gonna know we have it unless that thing makes some kind of sound! Sarah:[the T. rex looks over in their direction] He knows. [*CRASH* The 76 ball off of the nearby gas station rolls past their car]
Later, as the T. rex is chasing them, Sarah suggests that Ian should slow down so they don't get too far ahead of the T. rex and lose its attention. Ian takes one glance behind them to see how close the T. rex is and promptly hits the gas harder. A nice call back to the last time he was in that position.
Also from the T. rex's rampage we have a man doing a GodzillaShout-Out, saying "I left Japan to get away from this!" in Japanese.
During the scene where the T. rex bites the traffic signal, sharp-eyed viewers will notice that the street sign on the right reads "No Skateboards, No Dinosaurs".
Malcolm asks Nick why he joined Greenpeace. His answer: Women. Malcolm's response: "Noble, very noble."
When they first get to the island, they go into the jungle and find Sarah's backpack. Ian starts shouting, "Sarah!" and Nick yells, "Sarah Harding!" Ian stops, gives him a look, and asks, "How many Sarahs you think there are on this island?" Gets a call back later — when they're searching for Nick, most of the group is just yelling "Nick!" while Ian absentmindedly chimes in with, "Nick Van Owen!"
Roland Tembo has quite a bit of trouble with the pronunciation of the dinosaurs' names.
And later it seems like his team is having fun with his explanations:
Stark: Say again, Roland, a what?
Tembo:[throws the guidebook away] The one with the big red horn. Pompadour. Elvis!
When the group, looking for Sarah, finally sees their first dinosaur and naturally, Eddie and Nick are slack-jawed while Ian is unimpressed. Ian asks them why they're so shocked and Nick tries to explain that he didn't really think he'd see actual dinosaurs.
Malcolm: Yeah! Three cheeseburgers with everything on 'em.
Nick: No onions on mine!
Sarah: And an apple turnover!
During the T. rex rampage scene, it enters suburbia and starts slurping up the water of a backyard pool. A dog comes and starts barking at it but quickly retreats into its doghouse when the T. rex growls at it. This is followed by a child waking up and seeing it, then going to his parents' bedroom to tell them. They don't believe him at first, thinking it a normal childhood fear of the dark and eventually go to the bedroom to reassure him there's nothing wrong ... until they look out the window and see a T. rex right in of them, with the chain of the dog danging from its mouth along with the doghouse. The parents promptly scream; the child ... takes a picture of it.
When Burke describes the way Pachycephalosaur's skull is extra thick on the top of its head and is purposefully designed for absorbing impact. A second later, the Pachycephalosaurus helpfully demonstrates this point by ramming its head into a car door with enough force to send the two men inside the car crashing out of the windows on the opposite side. He then chases after Burke and pal.
Ian gets a golden Brick Joke line, after his daughter uses a complicated uneven-bars gymnastics routine to kick a Velociraptor out the window.
Ian:[incredulously] The school cut you from the team?
Possibly unintentional, but at one point someone runs into a room to hide from a raptor. The raptor responds by crashing in through the window. Quite similar to how the raptor in the first movie solved the problem of Grant and Company engaging the electric lock on the lab door.
In a Narm way, the Velociraptor attack on the hunter in the long grass. Ajay is yelling at the top of his lungs to not enter the long grass and ... he follows them into the grass to stop them. Then the hunters get attacked, but no one notices until they hear the raptor cries. One of the hunters looks up screaming wildly in a poorly acted way when he's jumped by one of them.
The "Characters" section during the credits of the film calls one character "Unlucky Bastard".