Revealing mistake: When Tim is looking at the 2 cups of water vibrating due to the T-Rex's stomping, you can see a very small dark spot at the bottom of the cup, which is actually the knot of a guitar string that was plucked to create the vibration effect.
Continuity mistake: When Nedry's car is stuck in the mud, he goes out front to grab his winch and pulls out a fair bit of wire. In the next shot, we see that he has a lot less wire than before, even though we never heard the winch retract.
Continuity mistake: When the baby Dinosaur is hatching, her arm comes out but in the very next shot it's her head that is coming out. (00:27:30)
Chosen answer: They all left on the same boat Nedry was trying to get on with the embryos. You can hear Samuel L Jackson's character announce that the boat will be leaving at a specific time and everyone had to be there or be left behind.
Shannon Jackson