When Woody, Buzz, and Jessie first encounter Mr. Potato Head's arm, it is clearly his left arm. However, when it is hooked onto the towel ring, it is his right arm. It then changes back to his left arm in the next shot.
Similarly to the stegosaurus/triceratops mix-up, Mr. Pricklepants is labeled a 'German beaver' instead of a hedgehog. This suggests both were deliberate.
On Ron the Manager's billboard of toys and other stolen items up for sale, the photo of Trixie is labeled "STEGOSAURUS", when she's a triceratops.
The motel manager didn't cross off Jessie's picture, despite the fact that she had been sold.
For some reason, Woody didn't use the paperclip to open the box, just like Jessie.
The motel manager wouldn't have stolen Bonnie's toys if they hadn't wandered off in the first place. Also, Bonnie should've kept her bag in the car.