The character Vellatrix makes numerous references to the "Harry Potter" franchise. This includes her name being a nod to Bellatrix Lestrange (one of the main antagonists of the series), and the magic school she serves as the Headmaster to "Snogwarts" being an obvious reference to the main setting of the series, Hogwarts.

Upon reaching Nuisance level with Lustat, one of her dialogue lines will have her claim that the player isn't "the cutest vampire slayer I've ever met", stating "There was this one gal in the 90s that... Well, best not to kiss and tell." This is a reference to the 1997 television series "Buffy the Vampire Slayer".

Generica's holiday outfit is a reference to the outfit worn by Jack Skellington, the main character of the 1993 stop-motion animated film "The Nightmare Before Christmas". When given said outfit, she'll state "What's this? What's this? This outfit reminds me of a nightmare I had once, just before Christmas.", which not only alludes to the film's title, but also to the song "What's This?" from the film, which is sung by Jack when he first arrives in Christmas Town.

In 2023, the game's official Twitter account hosted a poll to decide the name of a character set to be added to a future "Beach Bash" event (the character was tentatively named "Crab-chan" on account of her being "literally a crab turned into a waifu"). The options given were all crab-based puns: "Crabitha" (a portmanteau of "crab" and "Tabitha"), "Shelly" (a reference to how many species of crab have shells), "Pearl" (a nod to how crabs are capable of creating "pearl sacs"), and "Crabigail" (a portmanteau of "crab" and "Abigail"). The name "Shelly" ultimately won, and she was added to the game as part of the Beach Bash Event 2024.

Kira's photo unlocked at "Sweetheart" level was originally going to feature her holding a frothy mug of ale, but this was scrapped in favor of having her tug the player's shirt.

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. On top of this, three games that had previously crossed over with Yandere Simulator severed ties with the game:

• Glowstick Entertainment ended 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).
• 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.
• xDNA replaced the guest characters Ayano and Info-chan with reskinned original characters named Patti and Emily respectively.

The character Mur is a fictionalized version of Mur Moruno, one of the main artists of the game.

Amelia states in her Phone Fling conversation that she works for "Sad Panda / Happy Panda", an organization dedicated to the preservation of red pandas. This is not only a reference to Sad Panda Studios, the studio that made Crush Crush, but also to their mascot, which is a red panda. Further supporting this is one of the first text prompts the player can submit during the conversation which confuses the fictional organization for the real-life Sad Panda Studios.

The character Mio has an official VTuber Twitter, YouTube and Twitch channel, all run by developer Morgan Long.

Despite not winning the Vote-a-Fling event at any point, Lotus was added to Crush Crush as a datable girl to commemorate the release of Hush Hush: Only Your Love Can Save Them, where she appears as a major character. While Lotus' bundle normally costs $2, it can be acquired for free if you have save data for Hush Hush.

If you atone with Mio, there is a chance Mio will say "Quick - top five games! (Please don't say Fappy Bird... )". Fappy Bird is most likely a reference to the mobile game Flappy Bird.

When meeting Iro for the first time, the game will say that you were practicing for the Hangry Gamez, a reference to the The Hunger Games series of books and films.

Upon reaching Frenemy level with Bonnibel, she'll state "It's a piece of cake to bake a pretty cake. Just make sure not to use a messy recipe." This is a reference to the chorus of the song "Cooking by the Book" from the television series "LazyTown".

When flirting with Mio, there is a chance she will say "Your princess is in another castle... JK!" This is a reference to Super Mario Bros. when Toad says "Thank you Mario! but our princess is in another castle!" There is also a chance Mio might say "Player used Seduction. it's super effective. Mio fainted...". This is a reference to the "super effective" line used during battles in the Pokémon series. Mio will also reference both series in the game's "Uncensored Mode" DLC, through a Lingerie outfit modelled after Poké Balls featuring the "M" on Mario's hat, as well as a comment Mio makes upon selecting the outfit: "Mio used Hardened! It was super effective - *giggle*!"