When Pelinore enters the castle, he takes the glove off his left hand. When he's passing Wart, however, his right hand is the one that is bare. Immediately afterwards the bare hand switches back to his left.
When Merlin is packing his bag by magic to go to the castle, the flow of items stops halfway into the bag as the sugar bowl fights with the teapot. When Merlin says, "Where was I?" there are no items near the bag. The camera cuts to Wart and when it goes back to Merlin, the items are back where they were.
Throughout the entire film Wart's voice keeps on changing from being child like to adult like. One of the easiest spots to notice this is in the throne room towards the end when Wart is trying to get somebody else to take his place. He says "Oh! Archimedes I wish Merlin were here" in his adult voice, then the camera goes to a distant view and he calls "Merlin, Merlin" in his child voice.
In the scenes where it is raining outside Merlin's room at Sir Ector's castle, whenever Merlin steps in front of the window you can see the matte used to superimpose the live-action rain silhouetted over him.