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.
Factual error: Lori takes a screwdriver towards her 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.
Continuity mistake: When Jonas is swimming the tracking gun out to where the Meg is circling, he dunks his head under water to look for the shark. When he surfaces, his earpiece has changed ears. When they cut back to him, it's moved back to the correct ear.
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?
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: In the beach scene the fat boy is eating some ice cream and he has almost finished it when he wants to go swimming. A minute later in the water the ice cream is full and he is just taking the first bite of it.
Continuity mistake: During picking up her daughter with the submarine, her daughter's hair changes from wet to semi dry.
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)