The sharks in the movie are huge but in many scenes are not seen by the characters being attacked in waist deep water.
(at around 1h 28 mins) After Preacher is caught by the shark, he uses his cross to poke the eye of the shark; in later scenes, the shark's eye is fine.
(at around 1h 5 mins) Carter pries open a door with a knife that is on a sheath on his leg. The knife breaks and he throws it away. In the final scene (at around 1h 35 mins), when Carter and Preacher are laying on the wreckage, the knife is clearly visibly back in the sheath on Carter's right leg.
(at around 9 mins) When Carter is removing the license plate from the shark's mouth he is wearing fins. As he is helped from the water, he bends down and is wearing a pair of sandals.
(at around 31 mins) When they are extracting the protein from the shark, the monitor displays real-time MRI imaging showing the insertion of the probe into the shark's brain. This is impossible, since they removed the imaging device before placing the probe jig.
(at around 26 mins) The movie implies that swimming backwards is a maneuver the sharks figured out once they got smarter. Sharks don't swim backwards because they can't. They're built like airplanes; it's physically impossible for them to do it.
Many times we are shown people able to close doors even though copious amounts of water and air are rushing though them. This is clearly beyond the ability of humans. Their ability to do so cannot be explained by other devices attached to the door because those devices would have prevented them from opening the door in the first place.
Mako sharks can jump 30 ft. in the air, so the fences in the movie would have no chance to contain them if they wanted out.
Numerous times the sharks pound through steel doors and Carter provides an explanation about how much force the shark can build up. The explanation is sound except for the fact that shark skulls are mostly cartilage and would cave in on impact, killing the shark. This has actually happened numerous times in real aquariums.
(at around 1h 24 mins) When Carter is talking about what attracts a shark, he says that bright colors and the red fire extinguishers they found, should provide a distraction suitable enough to escape. In reality sharks are color blind, due to them only having a single wavelength cones in their retinas, where humans have 3 different types.
(at around 53 mins) When Preacher, the chef, is climbing up on the shelving in the kitchen to save Bird, you can clearly see the kneepads under his wet pants.
(at around 34 mins) Just after Jim Whitlock has had his arm bitten off and falls to the ground, you can see his real elbow coming up from his back under his shirt.
(at around 25 mins) Just before the experiment and moments before they witness the sharks swimming backwards, they are monitoring Carter as he swims through the protective tunnel. All of the cameras shown are fixed and mounted to the tunnel yet for a brief moment the camera monitors show a backwards tracking shot moving along with Carter, clearly shot by the film crew swimming in front of him. In fact a very similar shot is then shown as part of the movie, showing recycled footage being played on the monitors.
(at around 1h 35 mins) When Preacher shoots the shark with a harpoon, it goes through the shark's dorsal fin and supposedly impales Carter Black's right thigh. But in the next shot, just before the shark submerges, you can see the strapping arrangement used to fasten the harpoon tip on top of his leg.
(at around 3 mins) In the beginning when the shark is going for the swimmers that fell off the boat, the shark stops moving before he is shot by the shark wrangler.
(at around 1h 26 mins) Towards the end when the three remaining survivors try to get to the surface by escaping through the water filled shaft, when they are coming out of the shaft door, a crew members leg's and red swim shorts are clearly visible and in fact at one point block the entire shot. The three survivors at that point all had long bottoms and none of them were red.
(at around 1h 2 mins) As the elevator shaft starts to get flooded, Carter and Scoggins stay behind to shut the steel door. Just before they do, the green screen is clearly seen on the other side of the door.
When Susan is trying to get the shark away from the fence, she sliced her hand so it would bleed, then she jumped in the water - which wasn't necessary since she could have just held her hand over the water and let the blood drip.
Carter tries to save Janice by hanging upside down and reaching for her but the ladder below was still intact so all she had to do was swim over to it and climb up.