Continuity mistake: When Arthur is out hunting in the woods, Arthur is lying on a tree branch. In one shot, his pants leg is coloured brown, whereas, in the next shot, it is skin colour (as if he isn't wearing any pants). In the next shot, the brown pants leg has returned.
Continuity mistake: 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.
Other mistake: Merlin says, "Man will fly someday". For a few frames after he says this, his thumb on his pipe is painted blue, then returns to its normal color. This causes a blinking effect.
Suggested correction: No it doesn't. There's a tiny spot of blue noticeable for a mere frame, but in no way does his thumb turn blue nor could this be listed as a mistake.
Deliberate mistake: When Arthur is drawing letters of the alphabet, he only draws the outside of the letter A, not the horizontal stroke in the middle, yet it appears on the blackboard.
Continuity mistake: As a squirrel, Merlin's glasses come off & suddenly, it has ear pieces on the frames. When he places them back on, they're gone.
Continuity mistake: When Merlin is thrown in to the armor under the water as a fish, his glasses are thrown off and they land on the nose of the armor. The next time they show him, the glasses are down beside him. And still again, when Merlin is changed back into a human, he has the armor on his head and when he pulls it off, his glasses are on underneath the armor.
Suggested correction: Notice the dialogue just before Merlin turns himself and Arthur/Wart into fishes: Arthur: You mean you can turn yourself into a fish? Merlin: After all, I happen to be a wizard. If Merlin has the magical powers to turn himself into a fish, perhaps a by-product of his magic is that his glasses are magic, so he retains his glasses when he undergoes the transformation into a fish, even if his glasses fall off, they magically return to him, and his glasses magically reappear when he turns back into a human.
What's more likely - the director intended Merlin's lore to include magically retaining his glasses, or the team of animators made a couple continuity errors?
Continuity mistake: Arthur jumps over an enclosed fence to get to the Sword in the Stone. After he gets the sword, he runs out of an opening in the fence that wasn't there when he entered the area.
Continuity mistake: Merlin slides down the hill & skips across the water. As he crosses the water, there are a few large rocks in the water in the background. As Arthur skips across the water, there are no rocks in the water.
Continuity mistake: When the wolf slides into the water, after Arthur and Merlin, a big rock appears in the middle of the pond, that wasn't there when Merlin and Arthur crossed.
Continuity mistake: Arthur is seen looking at the birds flying with a pipe. In the next shot, the pipe in Merlin's hand has gone.

Continuity mistake: The letters A and B on the bottom row on the blackboard differ styles between shots, being wobblier in the second shot.

Continuity mistake: Before Kay cuts the mop's handle, the mop is dark brown. After he cuts it turns to vanilla coloured.

Continuity mistake: When Merlin searches for the model plane the knot holding it swaps from neat to crappy between shots. (00:56:02)

Continuity mistake: When Ector and Kay fight, the mallet behind turns 180ยบ. (00:49:30)
Continuity mistake: When Ector walks Merlin to the tower, the bones on the floor by the door disappear between shots. (00:20:47)
Continuity mistake: When the movie begins and Merlin prepares tea for Arthur, the amount and shape of the cookies on the plate changes between shots.
Continuity mistake: During tea, after Merlin commands the couch to come walking, the books on the table change positions between shots.
Continuity mistake: When Merlin enters his place and pours water into the pot, the bookshelf behind has a bottle on the upper right corner. A shot later the bottle has been replaced for a thick book.
Continuity mistake: When the movie begins a squirrel sits on a tree with dry and broken branches. In the following shot the branches look different, with small branches having suddenly appeared.
Continuity mistake: The first shot of Merlin's house shows a dark green pot on the top of the shelf behind. A shot later it's dark orange.