When Una steals the carriage to prevent Yvaine from crossing the wall, she is wearing her plain blue dress. But during the pursuit, shots of her (or the stunt person) driving the carriage show her wearing a protective black vest over the dress. The vest disappears when she reaches Yvaine.
After realizing Yvaine can't cross the wall, Tristan runs down the street (the shot is from the side). After some shots of other characters, Tristan is running down the street again (the shot is from in front). However, the part of the street he runs down initially is a part he had already been running down.
After Yvaine is captured and Tristan reaches Ditchwater Sal's carriage, a saddle appears on the horse that was pulling it.
When Tristan pulls Yvaine off the road to avoid being seen, Yvaine has her cape on. But when when it cuts to a side on view, her cape is gone.
When the king takes off the ruby necklace, he lifts it over his head without unclasping it. When Yvaine puts on the necklace, she has to unclasp it in order to fit it around her head. The necklace then rests against her collarbone; if it had remained its original length, she would have been able to slip it over her own head and it would have hung down a great deal further.
Yvaine refers to the little creature in the caravan as a mouse. The creature appears to be a dormouse, a rodent that is similar, but not identical, to a mouse. However, Yvaine is a star who, though she has been watching earth for some time, should probably not be expected to know the difference between rodents, especially when most humans cannot tell the difference either.
When Mormo and Empusa are talking to Lamia in a mirror (and telling her that the star has returned to Earth and is also being pursued by a prince), the scene is shot from above. It is clear, however, that Mormo's words are not synched with the sound. In one shot she is saying the same thing but out of synch. In another, the sound of her speaking is not related in any way to what she's saying. Though not actually stated much in the film, the reflection of the witches in the book is always a reflection of their younger selves.
When Lamia is laughing, there is a close-up shot of her mouth. All her teeth are dirty except the back few on each side, which are stark white.
When Ditchwater Sal cuts the rabbit into "heads" and "tails", the rabbit is clearly in three pieces - with the center small piece cut on both sides (not simply broken off one or the other half. It had obviously been cut in a previous take.
When Empusa and Mormo are dragging the alligator out of the cage, the clear tape keeping its mouth shut is visible.
When Septimus is holding the knife to Bernard's throat, the knife blade's position alternates from behind Bernard's ear to his face and back again as the PoV of the scene changes.
When Tristan wraps the chain around a tree, one end is tied to Yvraine but when he clasps it together an open end of the chain appears out of nowhere along the bark.
When Yvaine and Captain Shakespeare are dancing, Robert De Niro's hearing aid can be seen in his ear.
When Captain Shakespeare is playing the piano with Yvaine, you see him playing 3 notes on the piano (1st, 2nd, 4th). What you actually hear are different notes that make a perfect chord (1st, 3rd, 5th).
In the montage where Yvaine and Tristan are learning different talents, there is a piano being played. The audio plays major thirds, but the picture shows whole tones being played on the keys.
When the Bishop is talking to Primus about leaving quickly to find the stone before his brothers during the camera pan from the ceiling to the actors, the audio of the Bishop doesn't match his lip movements, but in the close-up shot everything realigns.
When the unicorn arrives to release Yvaine, it is untacked, and she mounts it bareback. However, in a following scene, a stirrup is clearly visible around her foot, meaning there is a saddle hidden under the drape of her dress.
After realizing Yvaine can't cross the wall, Tristan runs down the street. In a shot of him from the front, the dust and a tire track (presumably from the camera rig he is chasing) are briefly visible.
Near the beginning of the movie, there is a wide, rotating shot (from above) of Tristan and Yvaine walking on a road. Near the end of the shot, grass is being blown by the helicopter that was used to film this shot.
Lamia's hands reverted back to their old, decrepit state when she turned the boy into a goat and cursed Ditchwater Sal, which she noted as being "hardly extravagant." However, conjuring an entire elaborate Inn, which could be considered "extravagant", had no such effect on her.
Toward the end of the movie, Lamia uses a steel on the edge of her glass knife (presumably to sharpen it). Steels are only used to correct a curled edge on a regular knife. A glass or crystal knife's edge cannot curl, so a steel would not help, and might actually damage, the edge. This error was also present in Neil Gaiman's novel: in the commentary to the audio-book, he says that while recording it he noticed for the first time that he had made "a huge and embarrassing mistake in sheer physical science" when writing the novel because during a revision he had changed the knife from metal to obsidian (volcanic glass) but had left in the description of Lamia sharpening the knife on a whetstone.
When Lamia catches up with Yvaine at the Wall, she has the wool hat on her head as she gets out of the carriage. The hat disappears as she no longer is wearing it after Ditchwater Sal is dead and she forces Una and Yvaine into the carriage.