When Tyler and Anne are exploring outside the clinic, Tyler's voice is different than from the rest of the film (he's dubbed by Ted Rusoff for just this scene).
When Steve goes to search for his son, he starts up the helicopter twice.
Despite the title, the flying fish in this aren't piranhas at all. They are actually grunions, which are saltwater fish.
Obvious dummy when Ann goes into the wreck and the supposedly dead diver floats down on top of her.
In the wreck of the Earl Fitzgerald, the plastic dummy of the scuba diver floats up and bangs on the lens of the camera.
Police chief Steve Kimbrough's digital wrist watch is obviously for continuity reasons all the time in setup mode.
During the nocturnal piranha beach attack, wires can clearly be seen in certain shots holding up the flying piranhas.