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 Wart is climbing the small dead tree behind Kay on his hunting trip, he is wearing red tights. In the next shot he has bare legs, but then he has his red tights again.
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.
When Archimedes is teaching Arthur to write the alphabet, there is a point when Arthur moves to talk to Merlin and the "F" disappears. It then reappears in the next scene.
The Sword in the Stone is in an intact semi circular fence in a church yard. Wart runs to the fence and leaps over it leaving no foot prints in the snow on the ground. Having drawn the sword he runs out but the fence now has a gap in it and there are now foot prints in the snow.
Merlin perpetuates the myth that medieval people believed that the world was flat; in really, it was widely accepted that the world was a sphere.
When Mim is sitting at the table playing solitaire, she pulls the 3 of hearts from the deck, however the 3 of hearts is already on the table.
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.
When the sugar bowl flies to Merlin's bag, it is seen flying under the lid and spoon on the table.
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.
When Arthur as a squirrel falls on the broken tree branch after being pushed by the old lady squirrel, his mouth doesn't move the first time the yells "Help!"
After Merlin turns himself into a goat and headbutts Mim over the cliff, he is seen bleating yet no sound is heard from him.
When Merlin and Wart are fishes in the moat, a turtle is seen swimming around. Britain has no native turtles.
Arthur has an American accent, yet everyone else has a British accent.
The characters pronounce "schedule" the American way ("skedule") instead of the British way ("shedule").
Kay says he will shoot the deer "right smack through the old gizzard;" deer do not have gizzards, it is an organ generally only found in birds.