When Bo Peep gets taken away, the car driven by the new owner has the license plate RMRF97. it's a sort of meta-Toy Story 2 (1999) reference. It's an often repeated story that the second Toy Story film was nearly entirely lost when the main file was accidentally deleted from the main Pixar servers. This license plate references the computer command which nearly erased the movie. the Unix command "rm", with "rm -rf" standing for removing all files recursively in a given directory and without confirmation. Thankfully, a pregnant employee had a backup copy of the film on her home computer, which had to be gently driven to Pixar HQ in order to save the movie.

At the beginning, when Andy gives Woody to Bonnie, she reacts differently from when the same event was depicted in Toy Story 3 (2010).

Scenes over first part of credits further the story of Woody and Bo's new carnival gang followed by a scene showing what Bonnie made after her first day of first grade.

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