Visible crew/equipment: When Angel Marie comes up to attack Fozzie, you can very easily see the forehead of the puppeteer, as well as the T formed by the human hand merging with the puppet hand.
Revealing mistake: When Hawkins is pulled into the lifeboat by Long John Silver, if you look closely, you will see that it is a stunt double who is doing the falling.
Continuity mistake: In the scene where Long John Silver comes into the Captain's quarters to offer them all some brandy to toast the voyage, watch the glasses on his trolley. When he wheels the trolley in, all the glasses are on the right hand side. When he wheels it out (nobody but Fozzie having drunk any brandy), all the glasses are on the left hand side.
Plot hole: In the beginning after Flint buries the treasure, he kills all the men that are with him. The pistols he has are one-shot pistols, so there's no way he could kill 14 men using only two one-shot pistols.