In one of Harley Quinn's introduction lines to Mr. Freeze, she asks if he can "make her a pony", to which he retorts, "It will make the twilight sparkle." Harley Quinn then will say, "Hahahaha! I was hoping you'd say that." This is a reference to Harley Quinn's voice actress, Tara Strong, who also voices Twilight Sparkle in the series "My Little Pony: Friendship is Magic".
Contributed by RyuHane
In one of the possible intro dialogues between Batman and The Joker, Batman will ask if Joker is a "Scarecrow-induced allusion".Spoiler: This is a reference to Batman: Arkham Knight, where The Joker appears as a hallucination that's triggered by Scarecrow's fear gas.
Contributed by Boyobmas
Both Superman and Batman's "Super Moves" are a reference to their own Hollywood films.
When Superman performs his "Super Move" he'll beat his opponent in the sky, the same way he did with General Zod in their final battle from "The Man of Steel". And when Batman performs his "Super Move", he'll summon the Batwing to drag his opponent up to the sky, pausing in front of the moon to make the Batman symbol, the same way it did in Tim Burton's 1989 Batman movie, when Batman fought against the Joker.
Contributed by ProtoSnake
Hitting the opponent into the movie sign in the Gotham City stage enough times will have the letters spell out "FINISH HIM" and darken the background. A reference to Mortal Kombat, another title from NetherRealm Studios
At the end of Spoiler:Catwoman/Cyborg's Chapter, Spoiler:Catwoman will say the Brother Eye override authorization code, "LK-4D4", a reference to Mortal Kombat's Cyrax.