The U-boat is shown backing off the beach before the order is given to engage the propeller in reverse.
The amount of water in the plastic water-cooler style container increases significantly between the time they stop filling from the stream, and the time they are seen running away with it shouldered.
When Cole Stevens first leaves with the captain, he has the knife on his right hip. Later on, when they are talking together after seeing the T-Rex, knife is now on the left.
In the 11th minute when stack is knocked off the cliff by a pterodactyl, as he begins falling there is no bird near him. He also lands with his face already bloodied, when it was not bloody before the fall.
In the 8th minute as they land on the island, between shot there are four, then five people in the landing party. After they climb up an embankment, they are then showing back down on the beach with their supplies as if they had just landed. Then they hike up an incline trail without the embankment in sight.
When the order to start the engines and later to engage the propellers are given, all three of the remaining U-boat crew members are together on the bridge. The ordered actions must be executed in the vacant engine room, so it would be impossible for anything to happen as shown.
In the 69th minute after the T-Rex bites off the top of the guy holding the grenade, his remaining body falls over causing the ground to shake (as when the T-Rex walks).
In the 79th minute they reverse the submarine off the beach and back into the ocean. One cannot simply reverse a large ocean vessel after it has run aground.
All of the equipment used by the World War II German U-boat crew, most notably the small arms, are of American manufacture.
One of the German crewmen by himself carries a drum of either crude oil or diesel fuel. Depending on the exact contents and barrel type, this would weigh a minimum of over 300 pounds, and possibly over 400 pounds.
When the pool of crude is found, and the can is dipped into it, a closeup of the disturbed pool reveals that it is water with some dark stuff floating on top.
In the 79th minute when Frost fires the flare gun at the T-Rex, the sound of the gun firing precedes the actual firing.
In the 53rd minute when the captain says "We're all gonna have to work together," his lips do not match the dialogue. This happens often around this stage of the movie.