For the scene where Woody looks at the merchandise from "Woody's Roundup", mock-ups of the toys were shown to Tom Hanks in the recording booth. Hanks' spontaneous reactions to the toys were recorded and used for Woody's dialogue.
There was some discussion with regard to the song "When She Loved Me" and its place in the film. Randy Newman expressed concern over whether or not young children would be able to sit through the three-minute ballad while both Tim Allen and Tom Hanks admitted to being moved to tears by the scene featuring the song.
While driving around Al's Toy Barn, the gang drives down the Buzz Lightyear aisle. Tour Guide Barbie tells them "Back in 1995 short-sighted retailers did not order enough dolls to meet demand". This is an in-joke and a fact: When the original Toy Story (1995) was released, toy sellers did not think the movie would be a hit and they indeed did not order enough dolls to keep up with demand. The joke is also a self-deprecating dig at Mattel Toys, which denied use of the Barbie character in the first film, thinking it would be a flop.
When working on the film, someone entered a code called rm *, which, when entered, deletes everything on the computer as quickly as possible. Because of this, the creators of the movie lost ninety percent of the film. The animators tried to get the back-up animation, but it wasn't working. Fortunately, supervising technical director Galyn Susman had recently had a child, so she took a copy of the movie home with her so she could work from home. They covered the extra copy in blankets and drove it back to the studio, and were able to recover most of the film. Susman was laid off from Pixar in 2023.
The dust in the scene where Woody meets Wheezy set a record for number of particles animated for a movie by computer.