When facing off against Batman, Shaggy will say lines implying he and Batman have worked together before and are friends. This is a reference to the Scooby-Doo and Batman series having numerous crossovers that span all the way back to the 1970's.

In the game's Beta, Tier 15 of the battle pass features the rewards of Pajama Finn and the feline character Cake, both from the animated series Adventure Time. This is a possible euphemistic reference to the "Tier 15 of Dating" joke from the series episode "Burning Low" implying in-game that Tier 15 is bestiality, although it's never actually stated what Tier 15 is in the episode.

One of Velma's moves in the game consisted of calling the police to take the opponent away. This was changed on September 8th, 2022 with the release of patch 1.02. With the release of this update Velma will now call the Mystery Inc. gang and the Mystery Machine instead.

When sitting on his Chinese Lantern, there is a rare chance that Gizmo will sing Frank Sinatra's "New York, New York". This is an homage to a scene towards the end of the film "Gremlins II: The New Batch", where the near-entirety of the film's Gremlins sing the same song as a big musical number with the Brain Gremlin leading the pack and providing the vocals.

Despite MultiVersus being positioned by the gaming press and certain players disappointed with the latter game's lack of content as being a "rival" for having "killed" Nickelodeon All-Star Brawl, the development teams behind both games are fans of one another's work.

MultiVersus lead writer Eric Stirpē has stated that he writes each fighter as a "Multiversus version" by picking a point in a franchise's history for them to be chosen from by Reindog, in an effort to keep their dialogue in line with the source material. Some fighters from a single franchise are chosen from different time periods within it, but the points when they are chosen are not canon to the source material or the game's plot. It's unknown how every fighter fits into this writing guide, but it creates inconsistencies with some character designs in the game:

• Stripe and Gizmo were chosen just before Stripe's death in the first Gremlins film.
• Finn and Jake were chosen during the events of Adventure Time: Islands, though the lack of Finn's prosthetic arm is not explained, and Fern was chosen before he became a villain in Season 9 of Adventure Time.
• Steven and Garnet were chosen during Season 2 of Steven Universe.
• Bugs Bunny was not chosen, but rather emerged from hiding since the 1940s through a "hole in the page", with him being referred to as a "timeline hopper".
• Taz is from the 1990s (presumably tying him in to Taz-Mania).
• Marvin was chosen during the events of Space Jam: A New Legacy, and LeBron James was chosen two days after the end of the film.
• Tom and Jerry are from the 1960s, but are portrayed with a modern art style that does not resemble either the Gene Deitch or Chuck Jones runs of theatrical shorts from that time.
• Shaggy was chosen one year after the end of Scooby-Doo, Where Are You?, while Velma was chosen from an unspecified "cancelled 2000s reboot".
• The Iron Giant was chosen while returning to America after he re-assembles himself at the end of the film.
• Arya Stark was chosen during either Season 6 or 7 of the Game of Thrones TV series.
• Stirpē considers the DC Comics heroes and villains to all be original interpretations of the characters created for Multiversus.

When putting The Joker against Black Adam, the former will mockingly ask "Weren't you supposed to be 'rearranging the hierarchy' or something?". This is a jab at the 2022 film "Black Adam" starring Dwayne Johnson in the titular role. In the lead-up to the film's release, Johnson released a series of real life promos in which he declared that Black Adam would "change the hierarchy of power in the DC Universe". This quickly became an internet meme, and was poked at even further after the film bombed at the box office (the film had grossed $390 million, but needed to reach $600 million in order to break even).