With Nightcrawler and Dr. Doom being added as DLC, it caused continuity problems due to both characters playing major roles in the plot. To solve this, the game humorously lampshaded the confusion to explain why there are two Nightcrawlers and Dr. Dooms.

During the Murderworld level after rescuing Jean Grey from the Pitfall! arcade cabinet, Jean Grey's generic dialogue (when the player doesn't have Wolverine on their team) is used, but Nightcrawler has unique dialogue. Nightcrawler is at first confused why he is there when he is supposed to be missing, until it's implied by Nightcrawler that the Nightcrawler being used in Mephisto's Realm is a clone, and the one in the player's team is the original. Jean Grey then proceeds to speak of Nightcrawler as if he isn't in the room, leading him to assume she is experiencing hallucinations.

The boss fight with Dr. Doom instead has unique dialogue compared to other interactions with DLC characters. The game creates the plot twist that the NPC Dr. Doom time travelled from the future, and the Dr. Doom of the present begrudgingly joined the heroes to prevent the future Dr. Doom, who is powered by the Odinforce, from ripping apart the universe.