Not a real plothole but why did Miles and Nima search for Nedry just somewhere in the jungle? Wouldn't it be more reasonable to just walk back the road from the dock to the visitor center? I mean they didn't know what happened to Nedry and if I am searching for someone who should be arriving by car I would track down the road.
How did Dr. Sorkin get control over the Jurassic Park OS from her lab? I assume that the control room is the real control room otherwise this room would make no sense. So why should a terminal somewhere else provide access to the main program?
How did Explorer 02 get to the trike pen without crashing into Explorer 05?
Where were the Pteranodons from?
Why wasn't Dr. Sorkin much more afraid of the troodons or velociraptors when she knew that during the whole system shutdown all fences (including the quarantine pens) went down?
Why was the bone-shaker isolated in the jungle far away from the visitor's area?