Factual error: The men rowing the longboat into the wharf at Nassau are completely hopeless oarsmen. Needless to say, 18th century sailors would have been expert oarsmen. Untrained 21st century actors are not.
Continuity mistake: The scar on Singleton's face changes from the right side of his face to the left side several times.
Revealing mistake: The scene in the captain's quarters has water dripping from the ceiling. With the ship rocking from side to side, the water drops down perpendicular to the table the whole time, showing the scene is stationary and the camera is tilting. (00:14:00 - 00:14:35)
Continuity mistake: The governor is sick in bed. He is resting his head on a pillow with an embroidered pattern. On the next shot, the pillow is different and the fabric is solid. (00:14:00)
Character mistake: When Billy Bones gives himself in to the redcoats, he states he is Long John Silver. In one of the next cuts, he talks about Silver in third person. The governor shows no shock and they keep talking as if Billy Bones had said at the start of the conversation who he truly was. Then he instructs the governor on how to take on "himself" and Flint.