Continuity mistake: While Carter is trying to save Jane, he is a few feet above the water. But in a shot from above you can see that he has to bend his body so as not to touch the surface. It would be very easy for him to reach her. But in the next shot, he's high above the water again. (01:06:25)
Visible crew/equipment: When Preacher falls off the shelving rack into the the water after his bird was eaten by the shark, you can clearly make out the zip for his wetsuit under his jacket. (00:52:00)
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)
Factual error: The explosion at the end of the movie should have killed Carter, he simply couldn't have survived the concussion wave.
Continuity mistake: When Carter climbs the ladder to get out of the water after removing the licence plate from the shark's mouth, it shows a shot of his feet and he is wearing sandals. In the tank he was wearing swim fins. He talks to the big boss for a few seconds and the fins are nowhere to be seen. He then walks away with the fins in his hand. (00:08:55 - 00:10:20)
Plot hole: Considering the size and power of the sharks, why didn't the female just jump the fence at the end of the film. It was only 3 or 4 feet above the water at that point. (01:30:10)
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)
Revealing mistake: When Blake and Dr Susan McAlester (Saffron Burrows) emerge to survey the damaged research facility, you can clearly see coastline in the background, although earlier in the movie we see a weather map showing the facility clearly way out in the the ocean. (00:23:25 - 01:29:20)
Continuity mistake: Near the end when the survivors has reached the surface and LL Cool J gets attacked by a shark. Notice all the blood in the water. Shortly after, when he is pulled up and rescued, you see no blood at all. (01:28:20)
Revealing mistake: In the wet lab, just after the helicopter explodes into the tower, pieces of concrete are falling all around Thomas Jane, as he reaches to pull the blonde out of the water. The pieces of 'concrete' bounce all around like the foam pieces they are, not actual concrete.
Factual error: When the rescue helicopter approaches Aquatica, the pilot gives his call sign as "X-ray Alpha two eighteen." Numbers in aviation are read individually, so the pilot should have said "X-ray Alpha two one eight."
Continuity mistake: At the beginning, when Dr. McCallister is getting off the helicopter, she is wearing trousers, but when she is talking to Franklin, she is wearing a dress. (00:12:45)
Continuity mistake: When Preacher is talking to the Lord about his wrath, he is in a wide area of the corridor with "Sub Level 1-A" written on the wall behind him. In the next shot he is approaching the wide area with the sign again. (00:42:30)
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: When Carter and Scoggins are under water at the panel you can see light on Scoggins face when the camera is focusing on him. However when it cuts to Carter he is pointing his flashlight away from Scoggins. This happens twice during the shots. (01:13:45)
Continuity mistake: Even though the shark just jumped out of the water and ate the bird, the water is still when the preacher is falling into it. A big shark should make some waves in the water. (00:51:55)
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)
Continuity mistake: At the end, Carter manages to hold onto the perimeter fence, and the shark goes through. The shark then explodes, and Carter is seen being blown off the fence back the way he came, yet when he surfaces, he's now on the other side of the fence.
Visible crew/equipment: After Preacher says "Feeding time" and the camera moves toward the window, you can see the camera's shadow down in the left corner of the screen. (00:16:55)
Answer: They viewed her as a villain because it was her research that backfired and caused all of the chaos, even though none of it was intentional and it was a mistake. But audiences can be ruthless and unforgiving at times. However, the ending did feel like a cheap cop-out that created more plot holes. And many do feel she should have survived and completed her character arc. I don't know why they never offered the ending as a bonus feature on the DVD, but fans started a petition on the Change site calling for Warner to release the original ending. Thomas Jane is on board as well, as he's promoting it on his Instagram account. So that's probably the best way to get Warner's attention if you want to see the original ending.