At the beginning of the climactic fight with Peter, Hook cuts a couple of stems off the rudder wheel. When Michael and John and turning the rudder in the next scene, the stems are back on again, and disappear between shots.
At 38:42, for eleven seconds of the Peter Pan vs. Captain Hook fight, the picture is flipped, so Peter is fighting left-handed, and Hook is now right-handed, with his hook (normally on his right hand) flipped to his left hand. The first four seconds are from a distance, then it's a closeup. Their fighting shadows are also flipped.
John Darling gets a cannon ball blast near him on a hillock, he falls from there to water due to the blow of the blast, pirates pick him and take him to the mother ship on a small boat, but his hat doesn't fall anywhere in this entire charade and is intact on his head.