Continuity: When Shrek and the donkey are looking at the stars, in one shot Orion's Belt (three bright stars in a row) is right next to the moon, but in the next shot of the stars it's not.
Continuity: When Shrek sits to eat his meal he has a slug on the left-hand side of his plate facing towards him. When he is invaded by the Three Blind Mice the slug is suddenly facing the other way.
Incorrectly regarded as goofs: The Three Blind Mice are turned into horses to pull the coach after the wedding reception, yet they are seen moments later dancing on the organ keys. But other than the seamless continuation of the song there is nothing to suggest that the party scene immediately follows the happy couple's departure (there has been time to clear the tables for dancing) so perhaps the mice have discharged their coach-pulling duties and returned to the party for a boogie. While it's true that the sequence was added almost as an afterthought, and the final shot is of the coach being pulled by the mice/horses, we see no continuity error (the final shot is artistically "right" as a closer - that shot and the party need not necessarily be interpreted as being contemporaneous).
Continuity: Shrek and Donkey could not have made jokes about Lord Farquaad's height since they never saw him anywhere before except on a balcony. Shrek has never heard of him before, so cannot have known. (The producers acknowledge this oversight in the DVD commentary.)
Continuity: The chain around the dragon's neck disappears after Shrek uses it to climb on to her.
Continuity: The sun sets in different directions with respect to the same view of Lord Farquaad's castle.
Revealing mistakes: When donkey first meets Shrek, when Shrek confronts the knights, the shadows of the all people in the scene do not fall the same way, Shrek's shadow is casting more forward onto the leader knight, whereas the knight's shadows are off to their left.
Continuity: After Fiona changes to her "ogress" self when the sun sets at the wedding, shadows from the sun are still visible. However, she can only change into an ogress after the sun sets.
Continuity: When Donkey passes out (after the arrow incident) you see some dry leaves drifting up from the floor. However, in the next, wider shot there are no leaves to be seen.
Continuity: When Shrek is cooking weedrats over the fire, Fiona is already eating her weedrat. Shrek then sits down next to Fiona to eat. If you look at Fiona's weedrat on the stick, she hasn't taken a single bite out of it.
Continuity: When Lord Farquaad is questioning the Gingerbread man, he throws his leg onto the tray that it is lying on but when the camera shows the Gingerbread man, the leg is nowhere to be seen.
Continuity: When Shrek and Donkey are going to Farquaad's castle and they meet the mascot, it shows the mascot running back and forth through the roped-off lines at from ground level. Then it goes up as an aerial view, then back to ground level. The aerial view shows six rows, but through the combined views, the mascot runs back and forth eight times.
Continuity: As Shrek and Donkey are leaving we see them walk through sunflowers before the onions and cabbages. Later as they are walking back, the sunflowers are farther away from the castle than any other plant.
Continuity: When Fiona finishes off the rest of Robin Hood's Merry Men, she cries out a few seconds later that an arrow is stuck in Shrek's butt. However, if one looks in the few shots beforehand, there is none there.
Revealing mistakes: When Shrek and Donkey visit the Mini-Theatre in DU-LOC it takes a photo of them. After taking the photo, Donkey turns his head little. But in the next shot, the head is at same pose as in the picture.
Incorrectly regarded as goofs: Near the end of the movie, when Shrek and Donkey are rushing to make the wedding, Shrek climbs up the chain to get on the dragon. Previously, it has been assumed that the dragon then flies off, but if you look closely, the dragon lifts Donkey onto her back with her paw, and Donkey is present at all times.
Continuity: During the scene where Shrek and Donkey meet the mascot, after the mascot is on the ground, while looking through the doorway, the mascot isn't colored.
Plot holes: As far as we know, Fiona has spent her entire life alone in the tower, so she should have no knowledge of the outside world. Yet as her encounters with the songbird and Robin Hood demonstrate, she is more than capable of taking care of herself.
Continuity: When Lord Farquaad finds Shrek, Donkey and Fiona after Donkey discovers Fiona's secret, he gives Shrek a scroll, claiming it's the deed to the swamp. Later, when he leaves with Fiona, the scroll is nowhere to be seen.
Continuity: In the last two shots of the scene in which Fiona takes out Hood and his men, the swing that the Friar was in is missing from the background.
Incorrectly regarded as goofs: As Farquaad is already the ruler of Duloc, his quest to become king makes no sense. Why must he marry a princess? Can't he just give himself the title a la 'Napoleon Bonaparte'? Answer: because it's funny. This absurdity was probably written to mock the illogical, arbitrary rules that serves as plot catalysts in many classic fairy tales.