The Spanish privateers are noted as sailing under the 'gold and crimson' of the Spanish flag. However, the Spanish did not adopt a flag in gold and red until later into the 1700s, years after the film is supposed to be set.
During the final battle, Captain Blood's ship hoists a Union Jack flag, not in use until after the Act of Union in 1701. The scene takes place in 1689 (shortly after William III and Mary II take the throne). The correct flag should be the Cross of St. George (red cross on white background).
The courtroom scene is introduced by a shot of the royal coat of arms, in the form adopted in 1837. In the next scene, a window in the palace shows the shield correct for 1603-1707, reflecting the claim on the crown of France first made by Edward III of England in 1340.
When Arabella Bishop is about to take ship for England she is carrying a small dog, a Pekingese. The Pekingese was unknown outside of China until the late 18th century while the movie takes place in the 17th century.
When Peter Blood visits the two doctors in Port Royal, he puts his hat on one of the doctors' desks on the side furthest from the door. When he leaves, he walks to the door without picking up the hat, and as he turns at the door his hat can still be seen on the desk where he put it. But in the same shot his hat suddenly appears on his head and he doffs it to the doctors before walking out of the door.
When Blood and Levasseur are shooting coins, a single bullet hole can be seen in the ceiling following Blood's second shot. The next time the ceiling is shown, before any more shots are made, there are suddenly three bullet holes in the ceiling.
When Dr. Blood tries to leave the governor to meet his comrades before midnight, the clock chimes and wakes the governor. Blood turns to speak with the governor, holding his hat near his knees. When the scene shifts to the governor's perspective, Blood is holding his hat in front of his chest.
The Spanish pirate ship is shown flying a flag similar to the modern Spanish flag. The earliest use of this flag was 1783 for naval purposes, well over one hundred before the time shown. The correct flag at the time of the movie would be the Cross of Burgundy.
When Arabella Bishop is on the ship returning from England, she sees another ship in the distance, but the shot of the other ship was taken from land, not from the ocean, since we see waves starting to break in the near foreground of the shot.
The goof items below may give away important plot points.
When approaching Port Royal while the French are attacking, the lookout on Peter Blood's ship sees cannon fire from the distant ships. The audio is synchronized with the visual. At the distance from the ship to the port, the sound of the cannon would be delayed about 5 seconds for each mile.
While Lavasseur is lying in the surf after being killed in the duel with Peter Blood, waves splash over him from his head in the close-up, but from his feet in the longer shot. Also, the fresh blood coming out of the corner of his mouth is not washed away. It is still present and not washed away in the second shot of him at the end of the scene.