Following the game's release in 2013, it was featured on the "Clueless Gamer" segment on comedian Conan O'Brien's Conan talk show. During this segment, O'Brien was able to play as Superman with the "Flaming C" costume. "Flaming C" was a character co-created by O'Brien and DC Comics artist Bruce Timm, modeled loosely on O'Brien himself. When asked about the Flaming C skin in 2021, game director Ed Boon confirmed that a build of the game with the costume "exists somewhere", but the costume was never made publicly available.

In a Clash dialogue with Solomon Grundy and Hawkgirl, Solomon will call her "Bird-Nose" and reference their friendship in an episode of the Justice League animated series; "The Terror Beyond".

When Cyborg wins a round, he will shout "BOOYAH!", his catchphrase from the Teen Titans animated series.

When Superman's Red Son skin was first revealed, he still used the intro from his default skin. This was changed to the intro for his Blackest Night, Godfall, New 52, Man of Steel and Cyborg Superman skins.

The reveal trailer for Green Arrow was released the same day as the premiere of "Arrow" on The CW television network.

Green Arrow has a free downloadable costume based off of his depiction from the 2012 television series "Arrow."

Additionally when clad in this costume, Arrow's voice actor will change to Stephen Amell, his actor from the show.

When playing on The Watchtower level, Martian Manhunter will make an appearance to the far right of the Bridge in the background. However, he won't appear if he is participating in a fight.

After Joker defeats Regime Nightwing, he states that there has been a "death in the family." This is a reference to the 1989 comic of the same name.

Batman had his super move completely changed before the release of the game due to lackluster reception from fans. His original move was a parry attack, followed by several blows to the opponent and the use of his batclaw to hang the opponent for a final jump kick.

When a stage transition has been performed in the Great Hall area in the Hall of Justice stage, Darkseid makes a cameo appearance.

Concept art shows John Stewart as the represented Green Lantern, while in the final release, Hal Jordan was used instead. However, John Stewart did make an appearance as a downloadable skin for the Green Lantern after the game's release.

In the Fortress Of Solitude stage, there's an easter egg in which Doomsday (in the background) will have a costume on from the "Death Of Superman" comic, which cannot be used in game. In order to activate this easter egg, both players need to play as Doomsday. One player needs to choose his regime costume, and the other needs to choose his regular costume. The costume was added to the game later as DLC.

Flash's victory sequence is very similar to one of his "Heroic Brutality" moves from Mortal Kombat vs. DC Universe.

Aquaman's bio in the Archives incorrectly states that he can fly.

Deathstroke's pose when activating his super-move is based on the cover of New 52 Deathstroke #1.

Since the early versions of the game, the Metropolis stage has had a number of changes. The original time of day was daytime, but the weather in the final version is overcast. The TV in the streets had the Regime's logo which faded to Superman with glowing eyes and then back again. The final versions have just the logo. In an earlier version, it shows the Daily Planet logo as unfinished on the rooftops, but in the final versions it's shown completed.

The Joker, Ares, Black Adam , and Scorpion are the only characters in the game who kill their opponents after they win the fight. The Joker burns his foe, Ares throws swords at him/her, Black Adam severely shocks his opponent, and Scorpion stabs them with his sword and sends his enemies into the Netherealm.

Shinnok's Amulet, an item from Mortal Kombat commonly worn by him or Quan Chi, can be found in the museum at the Metropolis Stage.

In the Arkham Asylum stage, there are many references to the Batman Arkham series. The first is Hugo Strange in the background observing the fighters. He looks exactly like he does in Batman: Arkham City. The second is in the first stage transition (from the Main Hall to the Mess Hall) where the player is attacked by Scarecrow. He too looks like he does in Batman: Arkham Asylum. Finally, during the second stage transition (from the Mess Hall back to the Main Hall) where the player is beat up by Killer Crock, The Penguin, The Riddler & Two Face who also share their appearences from the Batman Arkham series.

When wearing the "Regime" skin, Superman's victory cut-scene has him ordering his foe to "Kneel before me!" This is most likely a reference to the famous line in Superman 2 where General Zod declares "Kneel before Zod!"