Factual error: After Stephen Maturin comes back with a small portion of findings from the Galapagos Islands, he presents a stick insect to Captain Aubrey, but stick insects (Phasmids) don't exist in the Galapagos Islands.
Factual error: At the end of the film, Aubrey sends the de-masted prize Acheron to Valparaiso, Chile, for repairs. Valparaiso is 3,000 miles from the Galapagos Islands, and, in 1805, was a tiny village without appropriate port facilities to dock or repair anything as large as a frigate. Valparaiso did not become a major port until after Chilean Independence from Spain (1810). Guayaquil (in modern Ecuador) would have been a more appropriate choice, being about 750 miles from the Galapagos, and being a major port in 1805. The choice between the two ports was moot, anyway, since both municipalities were Spanish territory in 1805, and thus were allied with the French, and hostile to the British.
Revealing mistake: The Acheron fires many devastating blows on the Surprise and the effect is visible in close-ups and a wide shot. However, after Mr. Mowett yells, "Relieving-tackles on the tiller! You men collect the wounded!" there is another wide shot of the Acheron in the foreground and Surprise in the distance. In this shot Surprise has NO damage whatsoever!
Revealing mistake: After a close-up of the drawing of one-armed Lord Nelson, Killick opens the lid of the steaming food for Jack in a close-up, just before Killick says, "Oh, here we go again. Scrape, scrape, screech, screech." Later, after Pullings takes command of Acheron, Jack tunes up his violin and Killick says, "Here we go again," in another close-up of the steaming food for Jack. Every detail of the food shown in both close-ups is exactly the same - obviously shot at the same time.
Continuity mistake: There are two tight close-ups of the words "hold fast," which are tattooed on Joe Plaice's fingers; When "Engaged enemy frigate at six bells," is said as Joe speaks, and as Stephen performs the brain surgery on Joe. The letters noticeably differ in the two shots, particularly the l, d, f, and t.
Continuity mistake: As Stephen holds the diary, in the shot facing him he begins to flip the page with his right hand, yet, in the next close-up of the diary he flips the page with his left hand. The actual pages he flips and the way he holds the diary differs in this and following shots as well.
Deliberate mistake: While performing brain surgery on Joe Plaice, Stephen, whose sleeves are rolled up to his elbows, reaches for a spoon with his freckled hand. In the following close-up it is blatantly apparent that it is not Paul Bettany's hand lifting the spoon, not to mention the bit of sleeve (not rolled up) that is visible at the bottom of the screen at the wrist. Then in the overhead shot the table with the instruments is visible, which includes the two boxes and silver spoon. In the next close-up the dark brown box's position and the spoon's position differ (before he picks up the spoon).
Factual error: In the brief shot of the Surprise underway after entering the Pacific, seen from dead astern and from above, the ship is leaving a respectable wake but is not heeling with the wind at all and the sails are hanging slack as though completely becalmed.
Continuity mistake: When Stephen comes on deck during the rounding of Cape Horn, Jack yells to him from the quarterdeck. Jack has his boat cloak on. He does not put on his boat cloak for several shots later, just after he tells Bonden to steer SSW.