The game has an entire debug mode which can be activated by setting the disc ID version field to 0x99 through using a hex editor and change byte #7 (0x00000007) of the ISO/GCM file. It works on all versions of the game.

The "forest map select" from Doubutsu no Mori still exists in the game's code, but there's no easy way to access it.

The train conductor 'Porter' is based off of the Japanese song 'The Monkey Palanquin Carrier'. This is the reason he's a monkey.

Within the game's data is an unused squirrel character, named "Shakitto" (シャキッと, meaning "crisp" or "crunchy") in the Japanese version's files. The text "Rya~" (りゃ〜) is also placed directly after her name, though it's unclear whether this is meant to be an additional component of it or if it was a catchphrase.

Despite Shakitto appearing to be a scrapped villager, her filename, ac_ev_dokutu, indicates that she was likely conceived as a special character. The "ev" component is used in the game's data for special characters that occasionally visit the player's town rather than being permanent components (e.g. Redd, Sahara, Wendell, Gracie, etc.), while "dokutu" is likely a truncation of "dokutsu," which can refer to either a cavern or a hole in the ground. The latter implies that she would've buried items for the player to dig up, similarly to an action that villagers can announce on the Bulletin Board in the final game.

Because no other code for Shakitto's intended function remains in the final game, spawning her in as a villager with Action Replay codes instead results in her using various bits of preexisting character data.

The NES games Balloon Fight, Baseball, Clu Clu Land, Clu Clu Land D, Donkey Kong, Donkey Kong 3, Donkey Kong Junior, Donkey Kong Jr. Math, Excitebike, Golf, Ice Climber, The Legend of Zelda, Mario Bros., Pinball, Punch-Out!!, Soccer, Super Mario Bros., Tennis, and Wario's Woods can be played in the game. They can be acquired through Game Boy Advance connectivity, e-Reader, and secret codes to Tom Nook. However some can only be obtained with the use of a cheat device which can also unlock all of them at once.