Audio problem: The last scene, when the captain and the doctor are playing music, the captain starts out with playing the violin with his fingers. Then the doctor is playing light tones with the bow on his cello. Suddenly, they switch, and the doctor is using his fingers, playing deep tones on the cello, and the captain is now playing with a bow. Finally, the first part of the music piece come back, and you hear both a violin (or some other small string instrument) played with fingers, and another violin played with a bow.
Continuity mistake: As Higgins studies the medical diagrams while sitting next to Stephen, when he turns the page he gasps and covers his mouth. The diagrams on the page in the close-up differ from the ones in the wide shot as Higgins still has his hand over is mouth. (01:27:50)
Continuity mistake: In the tent before and during the removal of Stephen's bullet, the ropes at the top of the tent behind Jack differ in the close-ups and wide shots. (01:30:40)
Continuity mistake: After Will's death, Joe looks through Will's belongings. As the shot faces Joe he unrolls the parchment and in the next close-up of the parchment, not only do the edges of it differ from the previous and following shots, the way he holds it differs as well. (00:53:55)
Continuity mistake: As Higgins removes the piece of cloth from the bullet and compares it to the shirt, the blood on his hands and the way he holds the shirt differs in the close-up and wide shots. (01:32:50)
Factual error: In the dinner scene, the captain points and asks the doctor which "weevil". Those are actually mealworm larvae (sold as reptile food in most pet stores in the US) and would never have been in a ship's food. Also, they show the doctor catching common green iguanas, which are not native to the Galapagos Islands. Neither is the species of tortoise pictured in the movie.
Revealing mistake: When the Surprise is disguised as a whaler, it burns smoke from the front end of the ship to make it look as though it is making whale oil. When it is chased by the French ship the smoke blows back over the ship. As they are sailing ships the wind is behind them which means the smoke should blow forward. (01:44:45)
Continuity mistake: When Jack and Stephen play their musical instruments, the cloth under Jack's chin changes position in the close-up. (00:26:55)
Factual error: The (authentic) book on Lord Nelson, that Captain Aubrey gives to Midshipman Lord Blakeney, wasn't published until 1806. The film is set in 1805.
Continuity mistake: After Stephen asks, "What is the weather gauge?" the table in front of Jack is visible in the following shots. As Jack extols the virtues of the Surprise the position of the nautical dividers in the instrument box differ once Jack is done. When Jack points to the shoals in the close-up, the map's position under another pair of nautical dividers, the log, ink well stand, etc., is different than the previous shots of the table. (00:18:30 - 00:19:55)
Revealing mistake: The characteristics of the scarring on Jack's left earlobe changes in quite a few shots. The scar, in the shape of the letter Y, over Jack's right eye changes its angles and as for the scar at his hairline, the upper and lower line switch off being longer in length throughout the film. (00:18:35 - 00:33:00)
Factual error: The version of the Lord's Prayer in the burial at sea scene is a more modern version, not from the Book of Common Prayer which would have been used at the time. (02:00:40)
Continuity mistake: The blood on Jack's shirt constantly changes during the final battle with the Acheron.
Factual error: As the Surprise attempts to weather Cape Horn, the wind backs westerly, so Aubrey gives the order to steer South. As the command is passed to the helmsman, he spins the wheel to the left - which would point the vessel Northerly, since the wheel would be turned in the opposite direction.
Continuity mistake: After fighting aboard Acheron, when Jack sorts through some rubble with his sword and as he is stabbed, the items on the ground differ in consecutive shots. (01:57:10)
Continuity mistake: When Blakeney and Padeen run into Stephen's tent, Blakeney says, "So I've made a few notes, if you want to see them," and he hands Stephen the diary. The way Blakeney holds the diary, as he hands it to Stephen, differs in the shot facing him and the next one facing Stephen, note the clasp on the diary. (01:34:15)
Revealing mistake: During the scenes when Jack and Stephen are playing their instruments, it can be concluded that they are not genuinely playing. This is most noticeable in their last scene, when strumming. You will notice that they will be strumming when no music is audible. (02:07:35)
Other mistake: If the scene in which Jack Aubrey gives the order "hard a larboard" [meaning the opposite of starboard] was indeed a rudder order (ie. turn the rudder in the direction commanded, which turns the ship the other way, in this case to starboard) the face of the compass wouldn't have rotated clockwise. The compass shows a southerly course, rotates clockwise, and eases to show an easterly course, which is a 90 degree turn to port.
Continuity mistake: When Lofty asks if the Acheron is like a pirate ship, in the wide shot Davies, who holds a pipe, grabs him up. In the next close-up, the pipe Davies holds is positioned completely differently in his hand. (00:43:35)
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)
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.