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. (01:41:20)
Continuity mistake: The position of the needle and thread lying on Peter's body differ in the wide shot and following close-up. (01:59:10)
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! (00:11:00)
Continuity mistake: As Killick trims the wax on the candle, in the close-up his hand is wet. However, in the next wide shot as he says, "He's been at it again..." his hand is dry. (00:54:20)
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.
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. (00:26:25 - 02:05:20)
Audio problem: After releasing the whaler prisoners aboard Acheron, Mr. Hogg shouts, "Now do your worst!" though his mouth clearly does not say that. (01:56:25)
Audio problem: While doing repairs on Surprise, Jack says, "Repair won't do here. I need those replaced," but his lips don't move when his voice says, "..replaced." Then as he says, "Ask Mr. Lamb what he has in stock," his mouth actually says something else. (00:22:55)
Continuity mistake: When Stephen removes the bullet, the rope's knot on the pillow, to the right of Stephen's head, appears, disappears and reappears. (01:31:55)
Audio problem: After the Acheron attack on the Surprise, below deck Jack, Stephen and some others discuss the situation. When Mr. Allen says, "Triple-shotted at 200 yards, and our guns had no effect," his mouth is actually saying, "...at 500 yards..." (00:18:20)
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.
Audio problem: Jack tells Pullings that he will take the next watch. Pullings says, "Aye, sir. Mr. Mowett, Mr. Allen, calmly now. You know his orders," however he does not say the latter half of that sentence, he says something else. (00:42:55)
Continuity mistake: While Jack and the rest speak about Lord Nelson, the plate of bread on the table is visible when the wide shots face Stephen. The following two close-ups show the plate of bread on the table, as Stephen looks at the weevils and the bread is positioned very differently in these shots. As Jack slams his hand down on the table, the bread is positioned as in the previous wide shots. (00:32:45 - 00:34:25)
Continuity mistake: On Galapagos, as Stephen is being carried to the tent, after Jack utters the excuse of needing to stretch his legs, Mowett's position differs greatly in the two consecutive wide shots. (01:29:55)
Factual error: When the ships go around Cape Horn you see it in the distance. But the rock you see is not Cape Horn. Cape Horn is a 400 metre high rock face. (00:47:25)
Continuity mistake: While Stephen performs Blakeney's amputation, the string on the hinge of Stephen's eyeglasses changes in consecutive shots. (00:21:45)
Continuity mistake: After Killick sets down the platter of the 'Galapagos Islands', Jack says, "Gentlemen, I give you our destination." In the following close-up of the platter, the stack of china is to the left of the candelabra, yet, in the next shot, as Killick hands the spoon to Jack, the candelabra is farther back and the stack of china is towards the right. (00:59:00)
Continuity 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). (00:23:50)
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. (01:34:25)
Chosen answer: They stop singing because they hear Hollom joining in. There are very strict ranks in the Navy, and Hollom singing with the lower crew dissipates these ranks, which is undesirable. That Hollom sings with the crew is frowned upon by the captain, as can be seen by his serious/agitated reaction after Stephen mentions that Hollom has such a clear voice.