Continuity mistake: When Dr. Doppler and Jim first observe their ship, Dr. Doppler is right next to Jim when he points it out. When the shot changes to a long shot, they're much farther apart. (00:16:55)
Continuity mistake: Sometimes the "warped" patterns of glass in Amelia's cabin change, and after being replaced from the Surpernova (in which we see glass being shattered and that is the only glass in the ship that we see) every pane is warped.
Other mistake: In the beginning of the movie where Baby Jim is talking about Treasure Planet, he crawls under the top sheet of his bed that has been folded half way up the bottom of the bed, and peeks out the bottom. That's fine and all but then his mother straightens out the sheet and covers him up. You then see that the part he just peeked out of was the folded part so he shouldn't have been able to peek out.
Continuity mistake: In the scene when Mr Arrow is telling the crew off for fighting, in one scene Mr Scroop has a mole or something on the left side of his face, then in the next scene it's gone, then it's back on again, then it's gone for the rest of the movie.
Continuity mistake: When Jim is doing his flashbacks, Little Jim is sitting on the center of a rug. Then when he gets up for his dad, he has moved a bit, then when he sits down again, he has moved again. (00:34:10)
Continuity mistake: Captain Amelia is injured as the laser ball strikes the longboat that she, Jim and Dr. Doppler are escaping in. At first it appears her injury is quite serious and causing her a lot of discomfort. But when the pirates capture her and Dr. Doppler, and in the scenes where the pair of them are tied up, Amelia appears to be fine. But when the crew are escaping the exploding Treasure Planet, Amelia is clutching her ribs and is obviously unable to drive her ship, seeing as Dr. Doppler is doing so. And when Jim has saved everyone and the crew are congratulating him, Amelia is fine again.
Continuity mistake: In the lens of the spyglass, Jim climbs out of the barrel, and two things happen after this: One, the spyglass moves from being close to the corner of the table (about 1 1/2 inches) to several inches away before Jim hits it with his hand. And two: As Silver confronts Jim in the galley, Jim backs away, and there's a shot of the table where the spyglass has completely disappeared, and a plate, cup and some type of pliers appear.
Continuity mistake: In the center of the planet, there is a scene in which Jim is helplessly hanging on a wall and Silver holds on the ship full of Flint's treasures. In the wide shot John Silver and Jim Hawkins are far away from each other, in the next close up the can almost touch each other, and in the next wide shot, they are far away again.
Plot hole: During the nova scene, everyone is tying down the sails after securing themselves with lifelines to the mast. Jim and Silver are on the front and Silver is knocked off. Jim is then all dramatic and runs to grab Silver's lifeline which seems to be coming from above, and pulls Silver up like a pulley. How come? The lifelines were attached to the mast, so Jim's action is pointless... even if he could do it, because a shot later both lifelines are streaming right to the mast, leaving no room for a pulley of any sort.
Continuity mistake: In the scene where Jim and Dr. Doppler first meet Silver, Silver tucks in his shirt. In the next shot, it's still tucked in, but in the next, it's not.
Continuity mistake: When Jim, Doppler and Amelia are in the longboat and it is hit by a laser ball, you see Amelia clutch her left arm where she is injured. Next, with both hands, Amelia steers the boat. When on land she starts to step forward but grabs her ribs (seemingly in pain) with her right hand and falls, bracing herself with her left hand. Her left arm was later in a sling. Where exactly WAS she hurt?
Continuity mistake: When Captain Amelia is sliding down the rope and then flips, the rope she lands on is the same rope.
Audio problem: When the ship is being pulled into the black hole, Captain Amelia says "Hold onto your life lines gents. It's gonna be a bumpy ride." You can see her mouth is moving differently to what she is saying.