Continuity mistake: In the scene immediately following Fiona's thrashing of Robin Hood and his Merry Men, Shrek is holding Donkey and they are staring at Fiona in disbelief. When Shrek drops Donkey and turns to follow Fiona, you can see his entire backside and it's unpierced. In the next scene, Fiona discovers an arrow in his rump that wasn't there before.
Factual error: Lord Farquaad wants to marry a princess to become a real king. The mirror shows him three princesses to choose from: Cinderella, Snow White and Fiona. But Cinderella wasn't born a princess! In fact, her only chance to become a princess was to marry a prince.
Continuity mistake: Sometimes Shrek's front door opens outwards, at other times inwards, yet it can't be "two-way" because whenever it closes, it slams against the frame.
Continuity mistake: At the start of the film, Shrek is painting his "Ogre Beware" sign, you will notice that quite a bit of the top left corner of the board is missing. When he hangs the board on the post it is the opposite corner that is gone. He did not paint on both sides.
Continuity mistake: The dragon flies down without a chain, then there is a chain dangling for Shrek to climb about to go to the castle, and while the dragon is flying, the chain is gone again.
Continuity mistake: In the scene where Donkey and Shrek are crossing the bridge to rescue the princess, Donkey trips and breaks a board. In subsequent shots sometimes you can see a little bit still stuck in the ropes, and sometimes it disappears.
Continuity mistake: At the end of the film, the three blind mice are turned into the horses for the onion carriage but a second later they are dancing on the piano.
Deliberate mistake: When a glass of milk is poured, if you look closely, the glass is filled but the level of milk in the bottle doesn't seem to lower.
Continuity mistake: In the scene where Shrek and Donkey are on the wooden bridge, when Shrek starts rocking the bridge, we see that the castle is still quite a way off. However, Donkey only takes a few steps to get to the end.
Revealing mistake: In the scene where Shrek and Donkey are sitting by the fire and looking at the stars, when Donkey asks Shrek about "our swamp" and Shrek is telling him "there's no we, there's no our". When Shrek blinks, you can see his eyeball slicing through his upper lid.
Continuity mistake: In the scene where Farquaad's men are chasing after Donkey and run into Shrek, their leader is holding a scroll. In the next shot, it completely disappears without him moving it at all.
Continuity mistake: During the scene where Fiona pulls the arrow out of Shrek, Donkey faints. When he hits the ground about 6 leaves float up from the ground as if Donkey had fallen into a pile of leaves. When we next see Donkey laying on the ground and when Shrek picks him up, there are no leaves on the ground, they disappeared.
Factual error: As Shrek is sitting near the sunflowers field and staring at the Duloc (and day becomes night), we don't see the cathedral anywhere. It should be visible as such a big building, due to how big it is seen later, it should be very distinct over the houses' roofs.
Plot hole: Shrek tells Fiona how short Lord Farquaad is, even though in the film he only saw him when he was high up on the balcony. Although his height may seem like something well known throughout the land, Shrek never even knew about Farquaad before going to his castle. He even refers to him as "this Farquaad guy.".