After Molly destroys the bridge, and Andy says "Run for your lives" to the camera, Mr. Potato Head has both eyes, despite being shown seconds earlier as One Eyed Bart.
When Barbie removes the screws from Buzz's back and they reset him they rush to escape and never reinstall the screws but his cover stays closed.
When "demo" Buzz escapes from under Rex and Hamm, and is running to get away from the toys, he opens his left arm to call out to Star Command, saying he is being held captive by his own prisoners. When Buzz thought he was the real Buzz Lightyear (in the first film), he always pressed the red button on the right side of his chest to call for Star Command.
When the "caterpillar room" children go outside for recess, the clock shows 3:00. When they return to the room for Andy's toys' first playtime, the clock shows 1:00.
The Wild West train locomotive's motion wheels have been stopped by Woody in the opening scene, but are shown running in a short time later (in two different sequences).
Mrs Potato Head is missing her right eye for most of the film and complains that it was left "somewhere dark, and dusty". Later, when Mr Potato Head escapes from 'The Box', he is able to maneuver all of his parts to the tortilla, including his eyes. Since Mrs. Potato Head is essentially made from the same molds as Mr. Potato Head, she should have been able to maneuver her eye out of the dark.
The Post-Net bar code on the "State University" envelope (addressed to a Pixar office) which is moved out of the way by Woody to reveal the old photo, is not validly formatted.
In the novelization of the film, the phrase that is said when Bonnie presses a button on Buzz is "Buzz Lightyear to the rescue!" The actual phrase that is said is "To infinity and beyond!"
The label on Bonnie's backpack says "1225 Sycamore". A label that has an address on it should state the house number and street name. Therefore, Bonnie's label should read "1225 Sycamore Street".
When Lotso removes Mrs. Potato Head's mouth, she is unable to use it. This might contradict many other instances in which the Potato Heads are able to use their body parts when not connected to their body, but it seems that Lotso is also squeezing Mrs. Potato Head's lips together to impede her speech.
The toys never let people know they are alive, but several escape attempts, patrols by Lotso's gang and other things are recorded by the security cameras at the day care center. It is possible to alter images seen on security cameras, and conceivable that one or more of the toys in Lotso's gang would know how.
When the toys are taken to the curb to be picked up by the garbage truck, there are three garbage bags. When the garbage man picks up the bags, there are only two. Andy puts the toys in the third bag and when Woody splits open the two remaining bags they are full of garbage so are obviously not the bag with the toys in. The toys must take the third bag with them during the escape.
Lotso pleads for help in the compactor scene. When his arm is seen rising from the trash, the platform is moving towards the compactor. The camera switches back to Woody who is trying to make a decision. When the camera switches back to Lotso, the platform appears to be moving away from where the compactor is, backwards. This effect of an apparent change in direction is caused by the fact that the magnet strip above is moving faster than the garbage platform below, as can be seen in previous scenes.
When Woody is taking away by Bonnie, she puts him in her backpack and Woody is unable to open the zipper to escape. When Bonnie brings Woody to Sunnyside, Woody unzips her backpack fine. However Woody doesn't try to unzip her backpack in the film.
After Buzz dances around Jessie in the shrubbery, Woody and the others run towards the garbage chute. Meanwhile, Buzz stands in the background against the barbed wire fence. Parts of the fence have been animated in front of him despite the fact his body is clearly standing in front of it.
When Andy's mother writes "College" on one of the boxes, it is in all capital letters. Later, when Mrs. Potato Head sees Andy in his room, the writing has changed to only a capital "C" with the rest of the letters being in lowercase.
When Mr Potato Head meets the other toys using his cucumber body, Bullseye rolls the plastic potato body towards him. The holes for his eyes, nose, ears and hat are visible but there is no arm or mouth hole.
When the children charge into the Caterpillar Room and grab the toys for the first time, Rex is immediately seen smeared with paint, before the paints come out.
When Woody is looking at Andy's high school graduation picture in his room, there is a concert ticket in the upper left corner of the screen and another one just below it for a band called "Humble Beginnings" both with a date of Saturday, November 17, 2009. This date fell on a Tuesday.
When Woody is typing Bonnie's address on the computer, he does not press all of the keys for "Sycamore", most notably the "A", despite the screen having the street name correct.
When Mr. Potato Head runs across the toy piano, music is heard from the piano, but the keys do not move.
When the toys switched Buzz to Spanish mode, his Spanish accent was different from the one that he had in the movie's trailer.
When Woody and Bonnie's toys calculate the distance between Bonnie's house and Andy's house, none of the surrounding streets are marked correctly on the map.
The computer map does not state the distances to walk from neither Bonnie's house to Elm Street, nor from Elm Street to Andy's house.
When the toys are close to the industrial shredder, Slinky Dog is first pulled to the ceiling. Realizing the pull is due to a magnet the other toys grab metal objects to get pulled up and escape the shredder. On the other side of the shredder, the toys release the metal objects and fall back to the conveyor belt, inexplicably Slinky is there with them and the magnet seems to no longer affect him.
When Barbie dresses up in Ken's astronaut suit to get the Buzz Lightyear manual from the bookworm, the scene starts with the audience only seeing the worm give "Ken" the manual. It seems odd that Barbie was able to speak to the bookworm to ask for it. Surely the worm would realize it is not Ken's voice.
There's an assistant in the Caterpillar Room at Sunnyside. It seems strange that she did not realize that Andy's toys were not suitable for the toddlers.
Woody and Buzz's voice boxes are working properly, despite the fact that it had been 10 years since the events of Toy Story 2.
When Andy told Molly to get out of his room, she said that his room will be hers in 3 days. However, Andy only had 2 days to get ready for college. The reason why was because his toys were at Sunnyside Daycare for 1 day, and they were at the garbage dump on the day before he left for college.
When Andy exits his van at Bonnie's the camera shows Woody's point of view inside the college box watching Andy taking the box of toys to Bonnie. However after Andy gives all the toys to Bonnie she looks inside the box and finds Woody there leaving it unknown how he got there from the college box.