Within the game's code are 22 unused reactions; while several of them are animations designed for interactions with Wisp, Gulliver, K.K. Slider, and campers, many others are standard emotions, leaving it unknown why these ones were removed. While additional reactions would be added in various updates, none of the 22 unused ones were among them.

Additionally, one unused reaction is the Shrunk Funk Shuffle; this was previously obtainable in Animal Crossing: New Leaf after obtaining all other reactions from Dr. Shrunk. Its presence in the game's code thus implies that at one point in development, players were intended to learn reactions from him like in previous titles. In the final game, players instead obtain them through a variety of methods (i.e. being taught them by villagers and Jack, purchasing Nook Miles rewards, attending aerobics classes for 50 days, and completing the Happy Home Paradise DLC), while Dr. Shrunk only appears as an occasional visitor in the Roost from Version 2.0 onward.

Shortly after the game's release in 2020, the government of China ordered gray market online storefronts to stop selling the game. While no official reason was given for the ban, fans and analysts speculated that it was due to players in Hong Kong using the game's customization features and online connectivity to broadcast messages in support of protests that were occurring at the time against changes to the region's extradition laws. Around the same time, the game was also used by Joe Biden's campaign team to advertise his candidacy in the 2020 United States presidential election by creating a dedicated island and customizable items.

16 days after the election in November, Nintendo updated the game's Usage Guidelines for Businesses and Organizations, significantly narrowing how they could use the game for advertising. This included a rule requesting that offensive content be refrained from being created in-game, along with a statement asking to "refrain from bringing politics into the Game." However, this rule does not clarify what "politics" specifically Nintendo wanted to keep out of the game, and it appears to be in effect for any content created after the update, as it seems that none of the Hong Kong protest content or the Biden campaign's promotional content were taken down.

To coincide with the release of Animal Crossing: New Horizons, PETA released a "Vegan Guide to Animal Crossing".

On the back of K.K. Slider's guitar are two stickers labeled "PASS," depicting doodles of Brewster and Dr. Shrunk. Though difficult to see due to their small size and the fact that the back of the guitar is only visible when listening to a requested song from K.K., the stickers reference locations where he performed in prior games: the Roost (where Brewster works) in Animal Crossing: Wild World and Animal Crossing: City Folk, and Club LOL (where Dr. Shrunk works) in Animal Crossing: New Leaf.

While New Horizons stands out from earlier games through the rebranding of male/female gender options as "styles," presumably to make the game more accessible for nonbinary audiences, the game still assigns hidden values to them that correspond to a gender binary. Specifically, picking the feminine style results in the player character bearing a dark stripe across their chest, apparently representing a bra. However, this cannot be seen in normal gameplay, as players of both styles wear a plain white tank top if they aren't wearing a shirt or a dress. At the time of the game's initial release, a glitch was present that allowed one to see the bra texture, but it's currently unknown if this can be replicated in later revisions of the game.

In a post from April 26, 2021 detailing the Version 1.10.0 update (which released two days later), Nintendo showed off a screenshot containing a villager house not seen in any previous revision of the game. While this led to speculation about possible new villagers, Nintendo clarified on their Japanese website the following day that this was done in error, and that this house would not be appearing in the update; the image was promptly replaced with an alternate screenshot.

Coincidentally, 16 villagers would be added in the Version 2.0 update, but none of them use the house seen in the removed screenshot.

Upon catching a squid, the message that pops up will say that it's "off the hook", referencing the duo Pearl and Marina from the Splatoon series.

There is an item in the game that was originally called "Switch". This item had it's name changed to "Light Switch" in a version 1.2.0. It's possible the name change came about so that players would not confuse the aforementioned item with the "Nintendo Switch" which is another obtainable item in the game.

The reason for the game's sudden shift from a town to a deserted island was as a result of Animal Crossing's director Aya Kyogoku wanting to bring something completely new to the series. Kyogoku believed that players were "moving to a new location that already existed," and "wanted to giving them a new experience and thought a deserted island would be perfect."