Factual error: Lori takes a screwdriver to the left hand side of her abdomen. The doctor says it just missed her liver and she has lost a lot of blood. The liver is on the right side of the body and nowhere near where she took the injury.
Factual error: Our heroes find a boat belonging to shark poachers, smashed to pieces by the Meg. Floating about in the debris are the bodies of a number of dead sharks. Sharks do not have swim bladders and dead sharks do not float - they sink.
Other mistake: At the end, the ship has exploded after the crash of the helicopter and the crew is in the water. The woman is picking up the people from the water in her surfaced sub. How is this thing propelled if both forward thrusters are above water?
Continuity mistake: When Mying is playing in the tunnels with her toy and sees the shark looking at her she drops both the ball and orange colored remote which is sitting on top of the clothes when the meg bites the glass. When her mom looks at the floor the remote and ball are alone on the floor neatly placed away from the clothes.
Continuity mistake: When Jonas is pulled from the ocean, after shooting the tracker into the Meg's fin, there is an overhead shot of everyone moving to the back of the boat to see if Jonas is all right. A moment later, just after Suyin looks down at him, the same overhead shot repeats. (00:55:20)
Plot hole: The movie establishes the narrative that megalodons have been locked beneath a layer of hydrogen-sulfide and that the first sub to penetrate that layer is their own research sub, thus allowing the megalodon to escape the hydrogen-sulfide layer for the first time in modern history. So, how could there be a megalodon present to at the very beginning of the movie, which interfered with the protagonist's rescue efforts?