Continuity mistake: When Stephen is pressed to examine the two weevils, in the close-ups facing Jack, even after he slams his hand down on the table, the spoon in the gravy boat leans to the side, yet, in the shots facing Stephen the spoon is at the handle. (00:34:50)
Continuity mistake: Jack Aubrey's hair changes in consecutive shots throughout the film. For example, when Stephen tells Jack, "Let me take a look at that brow of yours," his hair differs in the following close-up. (00:16:40)
Continuity mistake: In the last shot we see the Surprise make a sharp 90 degrees turn to follow l'Acheron to Valparaiso. It seems that the wind changes 90 degrees in the same instant, because it is not necessary to trim the sails, and the pennant keeps flying in the same direction relative to the ship. (02:08:05)
Continuity mistake: When Jack is peering through the magnifying glass at the chart, we see 'Hidden Reef' and 'Dangerous Shoals', but in the previous shot those two things are shown way to the left of where he is looking. (00:18:05)
Continuity mistake: In the close-up of the deceased, Mr. Allen lies right beside Peter and Blakeney's knees are visible above Peter's head, while he mourns over Peter. However, in the wide shot as Blakeney still stares at Peter, Peter and Mr. Allen are now much farther apart as Davies sits between the two. Peter and the hammock's position differ in his next close-up as well. (01:59:30)
Continuity mistake: The blood stains on the front of Jack's shirt change drastically in the close-up, when he is stabbed, as compared to the previous and following shots. (01:57:15)
Continuity mistake: During Blakeney's amputation, the cloth roll in his mouth changes position in consecutive shots. (00:22:15)
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. (00:48:30)
Continuity mistake: The order is given to closereef the topsail. But moments earlier, you see seaman doing just that, working on the last reef.
Continuity mistake: When Captain Aubrey's head is bleeding after being hit during the first battle with the Acheron, we see the wound just above his eye. However, when we see him next, the wound is farther down his hairline. (00:11:50)
Chosen answer: The flag is a signal flag, and is probably meant to signal that the ship is a whaler or engaged in fishing operations. Such flags were part of an international code, which, with some modification, is still in use today. (The flag is similar to the modern-day "Foxtrot".)