The source code for Doubutsu no Mori contains references to a variety of non-Nintendo Famicom ROMs that would not appear in the final game, including Arkanoid, F1 Circus, and most bizarrely, the bootleg port of Tekken 2 by Hummer Team.

When creating Doubutsu no Mori, directors Katsuya Eguchi and Hisashi Nogami set out to create a game "unlike any that came before", not fitting into any kind of existing genre. However, since it was required for games to be classified into one genre for the retail packaging, they decided to call it a "communication" game.

If the player installs external NES ROMs onto the Controller Pak and selects the "Save a Letter" option at the Post Office, the game will bring up a unique menu for viewing and deleting the ROMs. Because Nintendo never officially implemented a means of installing NES ROMs onto the Controller Pak, this menu goes unused in normal gameplay. The menu is also absent from Animal Crossing and Dobutsu no Mori e+, due to the player being able to delete the ROMs directly from the GameCube's main menu.

Additionally, in the iQue version, the menu's text is corrupted, with the title appearing as garbled characters and the rest of the menu being in Japanese.

A total of 199 music tracks were composed by Kazumi Totaka, Kenta Nagata, Toru Minegishi, and Shinobu Tanaka for Dobutsu no Mori.

Among the files included in the Gigaleak, a massive 2020 content leak of internal data from Nintendo, are models associated with Dōbutsu no Mori depicting three human characters not seen in the final game: two redcoat soldiers, one tall and one short, and a middle-aged woman in an apron. These characters appear to be early versions of Copper, Booker, and Joan, respectively, which is corroborated by the fact that the woman's filename is "oba," with Joan's sleeping animation being labeled "Sleeping_Obaba" in the files for Dōbutsu no Mori.

All of this appears to indicate that special characters were originally intended to be human before being changed to unique animals later in development; in the final game, the only humans that appear on-screen are the player characters. Copper and Booker would later reincorporate the scrapped redcoat motif in Animal Crossing: Wild World and Animal Crossing: City Folk.

In the iQue release, the Carp is recolored red.

The game was originally developed for the Nintendo 64 Disk Drive, and would've utilized the console's internal clock to track real-world time, making the game seem truly alive. However, because of the Disk Drive's commercial failure, Dōbutsu no Morí, like many others, was moved to a standard Nintendo 64 cartridge, with the internal clock being built into the cartridge itself.

Dōbutsu no Mori (Animal Forest) was the starting point for the Animal Crossing series. The game was the last first-party title to be released for the Nintendo 64 in Japan.