Plot hole: When Morgan and her Slave/New Boyfriend are escaping from the burning ship, which is going to explode any second, they emerge onto the deck, run up a flight of stairs, cross the deck to the stern rail, look about themselves, then dive overboard. They know the ship is about to explode and are desperate to get overboard. The railings are about a metre away from the hatch they emerge from in the first place - why not just jump overboard there?
Plot hole: Towards the end of the film, Morgan (Geena Davis) and Dawg (Frank Langella) are fighting to the death below decks, and Morgan pulls back a canvas sheet to show a cannon pointing right at Dawg's chest - and he stands staring at the burning fuse for a ridiculous amount of time, easily enough time for him to casually step out of the way and let the cannon blast away harmlessly. What an idiot.
Revealing mistake: In the final battle scene Morgan grabs a rope and swings from one ship to the other. She grabs the rope over her head and keeps the rest of the rope in front of her. The rope remains taut all the way to her waist. If she were really holding herself onto the rope, it would be dangle loosely below her hand. The tautness of the rope reveals the safety equipment used in the shot.
Other mistake: Isn't it weird how in the final scene with the 2 pirate ships, both of these ships are continuously blasting their cannons at each other, yet the sides of the ship show little to no damage throughout the entire battle? You would think that the parts of the ship that are in the direct line of fire would get hit.
Continuity mistake: Nearing the final battle, the crew is ordered to weigh anchor. The shots switch back and forth from the anchor being raised, to overhead shots of the windlass. The rope is actually being played out (lowered) on the windlass, while the anchor is supposedly being hoisted.
Factual error: At one point in the film, Morgan calls out "Riflemen, to me!". The film is set in the late 17th century. Whilst rifling had been invented prior to this date, it was still rarely used except on the most expensive weapons, and even then mostly used by specialists. It is highly unlikely that all, if any, of the pirates would have been armed with them, especially in the close quarter fighting they would have been expecting. The pirates would be more likely to be armed with the more common smooth bored muskets of the period, so "Musketmen, to me!" would be much more likely to be correct.
Other mistake: In the final battle between the 2 pirate ships, there is a shot below deck showing a cannon and a pirate being blasted backwards. A few minutes later this exact same shot is shown once again.
Other mistake: Shortly after Morgan has successfully won William at the slave auction and they are trying to leave, armed soldiers begin closing in on them. As she attacks a couple in a doorway, we get a close-up of a nearby horse, who is wearing a 1902 Universal Pattern cavalry bit in his mouth. Not made until at least a couple of hundred years after the film is set.