Continuity mistake: When Lamia is in the coach communicating with her sisters in the mirror, her image goes from old to young back to old again between shots. (00:59:40)
Continuity mistake: When Septimus attacks the redheaded farm boy, the position of his knife changes between shots, from the farm boy's throat to behind his ear, several times. (00:58:05)
Revealing mistake: At the end fight scene when Lamia is laughing, you can see that her teeth are only darkened in the front, not the rear. (01:55:10)
Continuity mistake: When Ditchwater Sal blows the door off her caravan, just after Una stops Yvaine crossing the wall, you see the broken pieces of door fall to the ground. It the next shot they are gone.
Continuity mistake: The pony pulling Ditchwater Sal's cart changes throughout the movie. This would be so as to not overwork any one animal. It is most noticeable in the scene when Una is driving the cart after Yvaine. When she is in the city, the pony has a white stripe all the way down its face; when it is galloping in the forest, it has two separate white spots on its face; and the pony that Tristan detaches from the cart and rides has one spot on its face. Also when Tristan detaches the pony, it only has on riding gear (a saddle and bridle), whereas earlier in the scene it only has on a harness for pulling the cart.
Revealing mistake: When Septimus stabs the Soothsayer at the shoreline, when he pulls his knife out, there is no blood on it. (00:39:40)
Continuity mistake: When Lamia fakes crying and pretends to let Tristan and Yvaine go, the back of her dress changes slightly. When she first turns round, through the criss-cross at the back, you can see the goldish coloured fabric. But in the next shot, the gold is gone and all you can see is black. (01:49:55)
Continuity mistake: When the Old Man who guards the wall whacks Tristan to the ground with his staff, the long shot shows him turn it upside down in a threatening gesture, but in the close-up immediately afterwards it's the right way up. (00:23:20)
Revealing mistake: Robert De Niro and Claire Danes have visible earpieces in their left ears when dancing on the flying ship. (01:15:00)
Continuity mistake: In the scene when Humphrey meets Tristan, who has brought flowers for Victoria, at night, there are two pails behind the men next to the side of the road. Previously, when Tristan first arrives, they were not there. (00:07:25)
Continuity mistake: In the scene where Septimus confronts Tristan outside the window of the three evil witches' dwelling, Septimus puts his fighting knife to Tristan's neck. However, Septimus lost the same knife earlier while swimming away from the Caspartine's crew.
Continuity mistake: When Captain Shakespeare is in drag, doing his fan dance before a full-length mirror in the foreground, Prince Septimus appears in the background in partial profile and slowly turns to his right to fully face the camera. The shot immediately cuts to a closeup of Septimus to get his stunned facial reaction, and he is again turning slowly to his right to fully face the camera.
Continuity mistake: In the scene, where Ditchwater Sal is turning Tristan into a mouse, he is carrying Yvaine's pelerine. But later, when she turns him back into a man, he is not carrying it anymore (and she promised him to arrive in the exact same condition as he was).
Continuity mistake: As Tristan approaches Lamia after killing one of her sisters, he walks past the dead Septimus whose sword is about a foot away from his head. When Lamia reaches into the pool to grab her voodoo doll, there is a shot of Septimus and the sword is now in his hand.
Continuity mistake: When Dunstan Thorn attempts to cut the enchanted chain off to free Una, in the close-up of his hand, both the chain and his knife are in his right hand. In the next wide shot, the chain is in his left hand. (00:05:10)
Factual error: In the scene showing Septimus swimming underneath the water after having dived through Capt. Shakespear's cabin window, you can see Septimus holding his fighting knife in his right hand. After a stroke or two he lets go of the knife and it doesn't sink.