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.
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.
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 sunk, it stayed there, and the occupants could have just survived as it was.
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 Motorala 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 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.
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 close up shots where you see her in the water up to the waist. To do this in paragliding, you need to boat to be moving. However in the shots you can clearly see that the actress is motionless.