In late 2023, Yandere Simulator creator YandereDev was accused of grooming a minor after the person in particular revealed several screenshots and audio recordings between them, prompting some of the game's developers and voice actors (including Michaela Laws, the voice of main character Ayano Aishi) to leave the project. Additionally, two games that had previously crossed over with Yandere Simulator announced that they would be severing ties with the game. First, Glowstick Entertainment announced that they would end all future sales of Dark Deception: Monsters & Mortals' crossover DLC with Yandere Simulator, as well as officially cancelling Ayano's Lovesick Labyrinth (a planned crossover between Yandere Simulator and Dark Deception, previously shelved). Later, Sad Panda Studios announced that they would be updating Crush Crush in order to replace Ayano (who had been added as a guest character) with an original character named Ayeka.

The toothbrush model in Yandere Simulator, a background prop with no in-game use, at one point had 5,592 faces, making it the heaviest model in the game, including characters and entire interior rooms. It is theorized that the model was originally made for photorealistic CGI in commercials, and had its polygon count shoddily reduced, as each individual bristle on the brush is rendered. Eventually, the model would be replaced, giving it the much smaller - albeit still-ridiculously high - triangle count of 994.

When deciding what Yandere-chan's real name would be, YandereDev originally considered giving her a name that meant "murder", suggesting names like "Satsu Jinsha" or "Jinsha Satsu". He eventually narrowed down his options to three names: "Ayano", "Ayane", and "Ayana", all of which have "yan" in the name which is also in the word "Yandere". He ultimately went with Ayano, as it had the fewest Google search results, and thus was less likely to get confused with somebody else.

YandereDev, the creator of Yandere Simulator, was originally intended to appear as a playable character as part of Monsters & Mortals' crossover DLC with Yandere Simulator. However, his inclusion was scrapped due to the devs feeling it would be out of place given that the Yandere Simulator DLC was intended to focus specifically on Yandere Simulator itself. Despite this, some fans believe that YandereDev's removal was due to various controversies surrounding him at the time.