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.
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)
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.
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.