Plot hole: How did the men on the ship get killed? The bridge was intact and the T-Rex was still inside the cargo hold. [A raptor escapes from the boat when it pulls in to the harbour, but they cut the scene from the film and now that bit doesn't appear to make any sense.]

Other: When they're on the island and the INGen helicopters are flying in, Jeff Goldblum takes the binoculars and looks through the wrong end.

Factual error: When the vehicle is hanging off the cliff and the glass at the rear slowly begins to crack, it does so like sheet ice (or conventional window glass). Safety glass in vehicles would either be laminated (in which case it wouldn't shatter at all), or it would break into a million fragments...

Visible crew/equipment: When Sarah and Nick return to the trailer with the baby T-rex, there is a shot of Nick carrying the rex towards the operating table. Look between the baby rex's legs - there are a series of wires leading from a opening in the anamatronic dinosaurs belly to a bulky device (presumably a battery pack) in the actor's pocket. Once you know where to look for the wires, you will notice them in many other shots in the film when various actors are holding the baby rex.

Visible crew/equipment: When the T-Rex is running rampant in the streets, we see a guy running away from it. He tries to run into a video store, and the shot is from inside the video store. Right before that guy gets eaten by the Rex, he runs to the door to try to open it. And when this happens, you can see the reflection of the cameraman in the glass on the door walking towards it.