Four pieces of artwork in the Japanese release of the game were replaced in the international versions:

• The Fine Painting ("Jeanne Hébuterne with Yellow Sweater" by Amedeo Modigliani) is replaced with the Basic Painting ("The Blue Boy" by Thomas Gainsborough).
• The Healing Painting ("Woman with a Parasol - Madame Monet and Her Son" by Claude Monet, a.k.a. "The Stroll") is replaced with the Classic Painting ("Washington Crossing the Delaware" by Emanuel Leutze).
• The Lovely Painting ("Portrait of Irène Cahen d'Anvers" by Pierre-Auguste Renoir) is replaced with the Quaint Painting ("The Milkmaid" by Johannes Vermeer).
• The Pleasant Feeling Painting ("Olympia" by Édouard Manet) is replaced with the Scary Painting ("Ōtani Oniji III in the Role of the Servant Edobei" by Tōshūsai Sharaku).

Of these four, the only painting whose reason for replacement can be concretely inferred is the Pleasant Feeling Painting. Its real-world equivalent depicts a prostitute lying nude in bed, which Nintendo of America likely deemed too mature for a child audience.

The Fine Painting that was replaced in the Japanese release is a different item from the one named the Fine Painting in the English release of Animal Crossing, which is based on Paul Gauguin's "Arearea" and is included in all versions of the game.

With the exception of the Classic Painting, the replacement artwork would become standard for later entries in the series; the only replaced painting to return in a subsequent game is the Lovely Painting, present in all versions of Animal Crossing: Wild World.

In the Japanese version of the game, all sixteen player character designs have black eyes, as was the case in Doubutsu no Mori. In the international release, however, most of them are altered to give them blue, green, or brown eyes; only two variants for each gender remain unaltered.

In addition to the multitude of NES games obtainable as furniture items, the player can also acquire a blank NES (a blank Famicom Disk System in the Japanese release). On the surface, it appears to be nonfunctional, and interacting with it simply brings up the text "I want to play my NES, but I don't have any software." However, in 2018, dataminers discovered that using the item actually causes the game to scan the GameCube's memory cards for externally installed NES ROM data. By downloading NES ROMs onto the memory card, it's possible to play them in Animal Crossing via the blank NES, including titles not obtainable in the base game.

Six years later, Twitter user Gloomyfates discovered that this is a carryover from the original Doubutsu no Mori, in which the feature was officially utilized by a sweepstakes in Nintendo Dream magazine in which up to 30 contestants could win Controller Paks containing Ice Climber (which is not present anywhere in the N64 game's data). This indicates that at one point in development, Nintendo planned to hold similar events for the GameCube version, distributing additional NES games via memory cards.

The ROM loading function additionally enables one to patch NES ROMs after they are loaded, which can be used to install mods for Animal Crossing itself via the memory card.

In the Japanese version, Dōbutsu no Mori +, two of the NES games that the player could obtain were Gomoku Narabe and Mahjong. The international release respectively replaces these titles with Soccer and Excitebike.

Due to a programming oversight, the player can wear down their axe by simply equipping it and repeatedly reading the bulletin board or entering houses. This is because the game uses both a hit counter and durability counter to measure how many times the player can hit objects with the axe before it breaks; hitting a tree updates the hit counter by one point, while hitting a hard object like a wall, sign, or rock increases it by three. When the hit counter reaches or surpasses nine points, the durability counter is updated by one, and when the durability counter reaches eight points, the axe breaks.

When the player presses A with the axe equipped, the game checks to see if they are facing a tree, a solid object, or blank space. Because swinging the axe, reading a sign, and entering a house are all tied to the A button, the game increases the hit counter because it detects a solid object in front of the player, but the durability check is overwritten by the other interaction. Consequently, it is possible to wear down an axe simply by reading the bulletin board or entering a house multiple times and then hitting the tool against an object. Conversely, it is also possible to reset the hit counter and thus prolong the axe's longevity by reading the board or entering a house so many times that the value rolls back over to zero.