Continuity mistake: When the shark rises above water with Jan partially in its mouth, its teeth are in about the level of her waist. As Carter grabs onto Jan, it moves its teeth up to the top of her chest. In the wide shot that follows, though, its teeth are back at her waist, then in the last shot of her being pulled underwater, they are up way higher again, at her chest.
Factual error: Without wanting to go into extreme details, the genetics and biochemistry of the entire film is flawed. No geneticist in their right mind would even think about using gene therapy - a technique which is not entirely successful yet - to increase the size of the gland. One would use any of multiple techniques to identify and clone the gene responsible for the protein in question. It is cheaper, more successful, and a lot safer and quicker to do. A copy of the gene could be inserted into E. coli and produced on a mass scale in a beaker on land. After the protein had been isolated it would not be able to be given to patients in a pill form because it would be digested in the gut (like insulin for diabetics). (00:05:20 - 00:48:55)
Continuity mistake: Carter pries open a door with a knife that is on as sheath on his leg. The knife breaks and he throws it away. In the final scene, when Carter and Preacher are laying on the wreckage, the knife is clearly visibly back in the sheath on Carter's right leg. (01:05:00 - 01:37:45)
Continuity mistake: When Preacher, Susan and Carter realise the only way out of Aquatica is to swim and they start filling the room up with water, Preacher holds out his hands to Susan and Carter. Carter then holds his hand out flat for Susan to take, and she puts her hand on top of his. However, in the next shot Susan's hand is on top and Carter's is underneath. (01:25:25)
Plot hole: Mako sharks have been known to leap out of the water, sometimes into boats. Therefore, it is quite possible, perhaps even more so, for these specialised Makos to jump.
Continuity mistake: In a scene near the end of the movie, Carter is swimming back to the wet lab through flooded passageways. At the beginning of the swim, his left shoe is completely untied - you can see both laces floating. In the next full body shot (where his shoes show) the shoe is tied again. (01:13:30)
Factual error: Late in the film, Susan is wearing rubber aquatic shoes. She goes to her quarters to retrieve the data and decides to electrocute the shark that attacks her. She takes off her rubber wetsuit and stands on it on the metal table to insulate her from the current so she doesn't get electrocuted herself. But, isn't she already insulated by the rubber on the bottom of her shoes? Was this just a reason to get her to take her clothes off?