During the early part of the movie, Laura, the protagonist's young sister steps on a shard of glass at a beach, it is seen to bleed into the water and attract a nearby piranha.
At the end part of the movie when Laura and her brother are saved and pulled into a boat she sits with both her feet soles in full view of the camera and there is no wound.
The ski rope that was used to rescue the girl from inside the 'sinking' boat suddenly became dozens of feet longer than it was, enough to stretch clear across the boat and down the other side under water and back up into the boat. There was only a few feet of extra ski rope when it was first tied off to the boat railing.
When Jake saw the tube empty, he swam to it. Shortly, when he was back on the boat, he is completely dry, including his shorts.
At the beginning of the movie, the Sheriff (Elisabeth Shue) falls into the water while investigating the missing boater. Shortly after that she is seen wearing a completely dry uniform.
(at around 1 min) The cliff-diver has blue shorts, but the overhead shot of him coming to the surface shows him wearing a white colored pair.
The 'sinking' boat which needed to be rescued was in fact in the middle of rocks and on rocks and not sinking at all. Once it partially sank, it stayed there, and the occupants could have just survived as it was.
When the naked girls are swimming underwater, they somehow are able to go without oxygen for a very long time.
To help Kelly from the sinking boat, Jake dove under water holding a walkie talkie. It would have been impossible to use the walkie-talkie because it should be shorted from being soaked in water. Jake however, was able to call his Mom on the walkie talkie to drag them from away from the sinking boat. As equipment used on the Sheriff's Dept. patrol boat on the water it would make sense the hand held two way radio Jake used was a waterproof Marine model walkie talkie like the Motorola EX560 XLS which meets JSI4 standards (submersible to a depth of 1 meter for 30 minutes) .
Although it is very likely that prehistoric piranha trapped in an underground lake evolving over millions of years in complete darkness would, like many deep sea creatures, have vestigial eyes, be true albinos (colorless like cave species) and have developed bio-luminescent capabilities, this would not occur without random mutations to the generic code. Unless there is distinct evolutionary pressure (competition, shortage of resources, visibility to predators, etc.), they would not necessarily evolve these changes (and vestigial structures only become as such if specific random mutations occur or there is a major energy cost to maintaining the active structure). However, things that are advantageous when unable to see would have to evolve for them to find prey, so it is realistic that the piranha developed a highly sensitive sense of smell, as is apparent from their swift attraction to blood from a significant distance.
The concept that a top predator could survive for several million years purely by cannibalism without an input of external energy is false. However, they could conceivably have survived if some source of energy was available to fuel the bottom of the food chain. As the underground lake was sealed from sunlight, one possibility is an ecosystem based on geothermal energy. Such ecosystems do, in fact, exist in the benthic zones. So, in theory, at least, the piranhas could have sustained themselves as top predator of a food chain that started with geothermal micro-organisms.
When Jake uses the ski rope to rescue himself and his girlfriend from inside the ship, the rope is shown being threaded through the railing on the deck of the boat, in addition to stretching across the entire deck. They would not go directly away from the boat as shown in the film, but yanked up to the deck via the railing.
When the paragliding girl is about to be attacked by the piranhas there is a set of closeup shots of her in the water up to the waist. To do this in paragliding, the boat needs to be moving. However, in the shots you can clearly see that the actress is motionless.
When Jake goes to rescue Kelly he opens the valves on 2 propane tanks releasing the gas in an attempt to ignite them. Propane tanks have an internal check valve that prevents this type of action and this could only be performed if the proper hose was connected, which was not.
Various bathers during the attack scene are not in a state of panic.
At 0:01:37 -When Matt unscrews his beer bottle cap the closed captioning reads: [cork popping].
While a guy in a white shirt carries half of a yellow shirted man's corpse to shore, the cameraman's shadow is briefly shown on the sand at the bottom left of the screen.
(around 20 min.) Camera crane reflected in an extra's sunglasses.
A stagnant cameraman is vaguely reflected on the side of Laura's trombone.
The camera's silhouetted reflection can be seen after Mr. Goodman dumps a piranha into a tank.
Laura cuts her foot on a broken bottle in the water, but never complains about it after being rescued.
At the end of the film the expert says the fish have underdeveloped sex organs and these fish are babies. However a fish's sex organs are internal and he wouldn't know this without dissection or a CAT scan.
One of the dive team refers to his dive fins as flippers, something an experienced diver would never do.