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.
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.