Plot hole: It is apparent that Shrek and Donkey have never traveled to the land of Far Far Away, yet Donkey immediately recognizes the "old Keeblers' place" when he should have no idea where it is or what it looks like.
Suggested correction: Donkey only thinks it's the "old Keebler's place." Puss in Boots then corrects him and says it's the Fairy Godmother's cottage.
Continuity mistake: When the King enters with the tea for Fiona and him, you see the cups ears are facing outward. He holds the tray with both hands. When he set it downs the one the king refers to as 'that's mine darling.' turns 90°, to face the king.
Other mistake: When the royal messenger informs Shrek and Fiona about the royal ball the scroll he is reading from is not open enough for him to be able to say what is written.
Continuity mistake: Fiona enters the study while her parents are drinking tea to tell them she's leaving. The doors are both wide open behind her and the hallway is completely clear. But when she leaves the room, she reaches down and picks up her suitcase in the hallway, which would have been visible behind her moments before.
Continuity mistake: When the cooks arrive with the food during the dinner scene they set the food down on the table, but in the next shot from above they are still walking towards the table with the food.
Continuity mistake: When Shrek and Donkey and Puss are in the potions room, they are stealing a potion which is called Happily Ever After. Shrek tells Donkey to keep watch, the door is ajar in the next shot it is wide open.
Continuity mistake: When Shrek and co. arrive, as the coach travels down the drive way you can see the door handle. The servant opens it. When donkey says 'I'm going to park the cart...' he jumps in and as it passes Shrek at the back, the handle is gone.
Suggested correction: Handle is always in place.