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.

Among the files uncovered in the 2020 Gigaleak, a massive breach of internal server data from Nintendo, are early assets for characters who do not appear in the final game:

• Early textures for Wisp and Blathers. Given that both characters would later debut in Animal Crossing and Doubutsu no Mori e+, the presence of these assets reveals that they were originally planned for the N64 game before being held off and redesigned for the GameCube ports. Both early models feature different faces for the characters, with Blathers in particular resembling Celeste, who would debut in Animal Crossing: Wild World (implying that her design likely drew inspiration from Blathers' scrapped N64 model).
• Textures for a scrapped female cat villager with the internal ID CAT13. As villagers were not originally intended to change clothes, her default outfit, a Beatnik shirt, is included in her texture pack. However, no other data for her is present, leaving it unclear what her personality was going to be. The CAT13 ID (also written as CATD in hexadecimal) was ultimately given to Ankha in Animal Crossing; it is unknown if the original CAT13 evolved into Ankha during development or if she was simply assigned the ID for the sake of convenience. In Wild World onward, which uses a new ID system, the cat13 ID (spelled in lowercase this time) is instead given to Stinky (whose ID was CAT8 in the N64 and GameCube installments).
• An ID for a scrapped bear villager, BEA3. No additional data is present in the leaked files, with their associated folder being completely absent, and no villagers in Animal Crossing reuse their ID.

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 international release of Animal Crossing overhauls the designs of two different characters due to their Japanese designs being evocative of black and Asian racial stereotypes. In Doubutsu no Mori and Doubutsu no Mori + (the Japanese version of Animal Crossing), Jane is shown to have dark brown skin, white fur, tired eyes, and large, pink lips, making her resemble a blackface caricature. Meanwhile, Chip's original design gives him squinting, slanted eyes and large glasses, which in combination with his buck teeth makes him unintentionally resemble stereotyped caricatures of Japanese soldiers in American propaganda during World War II. In Doubutsu no Mori e+, Jane and Chip revert to their original designs. Despite this, the photo in Chip's booth still depicts his international design, which would become standard in all later installments.

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.