When Pinocchio and the gang rescue Shrek and Donkey, Pinocchio has to tell some lies so Gingy could reach the locks by walking on his nose. In the next scene, Pinocchio's nose is back to it's normal size.
As Fiona and Prince Charming (posing as Shrek) are about to dance, the Fairy Godmother tells the musicians to play the song, Holding Out for a Hero, "in C minor". However, they go on to play, and sing, the song in A flat minor (or more accurately A flat Aeolian).
Puss In Boots rips Shrek's shirt open when fighting in the woods. His shirt stays ripped open for the next few scenes. But as the party arrives at the Fairy Godmother's Factory, Shrek's shirt is no longer ripped open. There is also no seam or other sign of mending.
When Shrek pushes open the door of his house when he and Fiona arrive home after their Honeymoon it opens so it swings inward. But when Donkey leaves, it swings outward and it's stopped by the frame, making it impossible for the door to swing inward.
When Fiona's dad is giving the tea to Fiona before the ball, the cup handles are facing outwards from the center of the tray, once the king picks up the glass, in the next shot of the remaining cup, the handle is pointing a different direction.
When Shrek and Fiona are in bed in the castle, she is lying
on her left side. After Shrek gets up and opens her music box, he looks at her and it shows her rolling onto her left side. She was on her left side to begin with.
When Fiona first sees her diary, after Shrek has looked at it, it is open in the middle. When she first picks it up, it is open at the beginning of the book. In the final shot, it is open at the end of the book.
During the ball, Fiona's mother sits on the right side of the screen on the throne and Harold is shown sitting on the left. When she and her husband are shown sitting together, they have switched places.
When Charming kisses Fiona, she responds by head-butting him, rendering him unconscious, but then he recovers and hands the magic wand to Fairy Godmother. At the end, when Prince Charming came across Doris, he appears as he has just woke up from unconsciousness, seemingly unaware of Fairy Godmother's death and the subsequent events.
In the first film, Fiona's clothes never change when she transforms back and forth between human and ogre. At the end of this film just before Shrek and Fiona change back into ogres, she's wearing a white dress. When the change actually takes place, her dress is green.
When Charming first pretends being Shrek, he convinces Fiona that his voice has changed. However, Fiona and Shrek have just heard each other screaming their names a few seconds ago. Fiona should've definitely realized that Charming isn't Shrek.
Gingi's legs which were broken off by Lord Farquhard in the first movie have been re-attached with strips of frosting. However during the torture scene Lord Farquhard made it a point to crush at least one of the legs into crumbs so there should be nothing left to re-attach.
When Shrek is talking to Donkey and the small white dog in Fiona's room after their fight, the dog can be seen on a couch, with Donkey right next to it. In the next shot, Donkey and the dog have disappeared.
When Pinocchio and the rest of the enchanted animals look down at Shrek, Donkey and Puss In Boots locked in chains at the bottom of the Turret, there are no visible windows. However, when Shrek looks at the Gingerbread Man and the castle he is looking out a window.
At the end of the film during the ball when the clock begins to strike midnight, the first shot of the clock shows that it is 9:45 not midnight. That shot of the clock is taken from above the clock looking down at the palace entrance steps. Therefore the clock hands are pointing left on the camera shots (appearing to show 0945) though in fact they point straight up, i.e. 12 o'clock.
The King and Queen are shocked upon Fiona's arrival, discovering she married an ogre, even though they were the ones who sent the messengers to a SWAMP. On top of this, they should have suspected something when their daughter arrived in a giant onion coach.
In the opening scene, Prince Charming didn't seem surprised to see that there was no dragon guarding the castle like the legend tells. It is weird, since in the previous film we learn that the greatest danger which caused the death of the many knights who attempted to rescue the princess was not the hostile climates in the way to the castle, but the terrible fire-breathing dragon which guards it.
The goof items below may give away important plot points.
When Shrek changes into a human from taking the potion, his original clothes are too big and he has to steal clothes from the man in the carriage. When he changes back into an Ogre at midnight, he's back in his old Ogre clothes.
Although Shrek, Fiona and Donkey's 200-mile journey to Far Far Away takes many days, Gingy, Pinocchio and the gang make the trip in an evening with time to spare. This is because Dragon flew them there, as we can assume from her presence at the end, when the credits are rolling.