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. (00:53:18)
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. (01:21:10 - 01:22:00)
Other 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. (00:16:00)
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.
Continuity mistake: When Shrek walks out of his house and finds the fairytale creatures, you can see the three fairies go into one of the tents that were set up. The shot goes back to Shrek for a minute and then goes back towards the crowd and the fairies are back in the place that they were before.