Jim sits on top of the inn, eavesdropping on Dr. Doppler and his mother. He slides off the roof to meet the turtle-like alien who crashed out on a ledge. When Jim carries the alien back to the inn from its ship, they are on a dirt road much further away.
In the center of the planet, Jim hangings on a wall while Silver holds on to 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, they can almost touch each other. In the next wide shot, they are far apart again.
When Jim, Doppler, and Amelia's longboat is hit by a laser ball, Amelia clutches her left arm. In the next shot, Amelia steers the boat with both hands. On land she starts to step forward, grabs her ribs (seemingly in pain) with her right hand, and falls, bracing herself with her left hand. Later, her left arm is in a sling.
Jim appears to have a scratch or scar under one of his eyes, depending on the scene. It's actually a bag under his eye, like the "shadow mask" over his eyes, used to accentuate Jim's hopelessness. It disappears in the last scene, when he is content with his life.
When Jim is chasing Morph into the barrel of space plums, the galley is empty. They are in the barrel for a few seconds (after Jim yells "Busted!") before Jim overhears the pirates discussing mutiny and from the tone of the conversation, it indicates that it's been going on for a while. How did they get into the galley without seeing/hearing Jim jump into the barrel or Jim noticing them?
As the crew is trying to escape from Treasure Planet, Jim decides to use a solar surfer to activate the portal that can lead them to safety. During this time, no one ever considers the much safer alternative of sending Morph to do this, who is significantly smaller and can seemingly transform into anything of the proper size.