Continuity mistake: When Kevin goes to the grocery, he buys Tide detergent. While walking home, the two bags break, but no Tide detergent falls out.
Continuity mistake: There's an electrical outlet on the wall below the window (aligned with the window shade's loop) in Sid's room near the Megadork poster, but when Sid throws Woody to the floor and raises the shade (before he scorches Woody's forehead with the magnifying glass), that outlet has vanished.
Plot hole: Isn't it rather strange that nobody outside the Howard family's small town expresses any interest in the confirmed discovery of a new human sub-species, the only one on the planet? Wouldn't it be more likely that their little backwater town would be inundated with every press and scientific organisation on earth, and that the Howard family would be the centre of the greatest publicity carnival of all time?
Plot hole: How does the little girl Nina know Ferdinand's name if only the animals can communicate with each other? They're all calling him Ferdinand before she "names" him that.
Revealing mistake: When Austin enters the bathroom at the casino, keep your eyes on the door during the scene - it opens by itself before closing. (00:31:10)
Continuity mistake: As Buddy walks out into the street at the start of the movie when the cat is playing dead, you can see several parked cars on the street behind him. When the van backs up to 'catnap' buddy, there are no parked cars. Then as the van drives off again, there is a different bunch of parked cars in the street. (00:03:54)
Continuity mistake: In the bedroom scene the girl is holding a clear cup full of beer. The camera goes off her and when it comes back she is holding a blue cup. The camera goes back off her then on her and the cup is clear again. [This mistake does not appear in the unrated version - the blue cup scenes were shot specifically to secure an R rating from the MPAA because the contents are obscured.]. (00:13:20)
Factual error: While Bridger is watching the film of the Mafia boss following Beckerman he signals for the film to be stopped so he can look at the close up shot of the man. He is watching a 16mm film shown through a bog standard projector - stop a film like that for more than two seconds without closing down the projector shutter (this doesn't happen - if it did the screen would darken instantly) and it will melt and catch fire. This doesn't happen.
Visible crew/equipment: When Pee Wee is chaining up his beloved bike you can see the long chain coming up through the bottom of the bike box. Full screen version only. (00:13:40)
Continuity mistake: Rumplestiltskin looks completely different in this movie than he did in the previous film Shrek The Third; Prince Charming momentarily talks to Rumplestiltskin in the tavern during the third film, and the character looks completely different, has a different voice and different demeanor.
Other mistake: When Adam comes in and says "when I woke up this morning, the pain was gone", Connie is mouthing his lines behind him.
Continuity mistake: After Mark is found, he runs into Kate's arms and hugs her and her sunglasses fall off her head, but then in the very next shot they're back on her head perfectly. (01:24:50)