Continuity mistake: When Ellen is on the boat, and sees the shark coming towards her, the distance between her and the shark does not look very far. When it cuts to Mike, Jake and Hogie in the plane, from their view the distance between the boat and shark looks much greater, about 60-70 metres. Also, only about five seconds later, the shark jumps out of the water and strikes the boat, the shark could not have swam that distance in such a short time.
Plot hole: Why does the shark EXPLODE when it gets stabbed by the boat in the end? It had a transmitter of electromagnetic energy designed to shock it rammed down its throat, nothing that would explode like that.
Revealing mistake: In the scene where the shark has Michael cornered in the old, rusted boat; as he's about to use his oxygen tank to rocket up to the surface, the shark breaks through the wall and when it does, a large number of thick tubes can be seen running into the shark to make it work.
Revealing mistake: When the shark is rammed by the boat at the end, right before it explodes it is too obvious that the shark is a model. Some signs are: the oversized dorsal fins, its mouth is bent at an unrealistic angle, and it doesn't have eyes.
Factual error: The shark that attacks the Brodys in the Bahamas is presumably the same one that kills poor Sean Brody on Amity Island (that poor kid can't catch a break). Ellen departs for the Bahamas after Sean's funeral and the shark follows shortly thereafter. So, the shark swims from Amity, an island off the North Atlantic Coast, down to the Bahamas in order to stalk Ellen, Mike, etc. in a matter of days. Hmmm. As Matt Hooper said in the first film, "fast fish".
Revealing mistake: As the boat sinks you can see the rope attached to slow the boat sinking and control how it goes down. (00:10:45)
Revealing mistake: When the shark explodes, in the last shot (from behind the boat) which shows him exploding it is painfully obvious that the boat is only a model and not the real boat from previous shots.