Good Bad Bugs: Thanos' ending is glitched in the arcade version; instead of being given the option to choose between two endings, both play back to back with Magneto's ending text. While this is fixed in the console releases, the Marvel vs. Capcom Origins version is broken due to being based on the original arcade build.
Harsher in Hindsight: Spider-Man's ending, full stop. To elaborate, Spidey comes home from saving the universe and Mary Jane tells him that she's pregnant, with Peter re-assuring her she and the baby are his universe. Then One More Day happened. Though before that, she already miscarried at the end of the Clone Saga
Memetic Mutation: Some of Spider-Man's lines, such as, "One for J.J.!" and "Do your job!" (or alternatively, "DO YOUR GODDAMN JOB!") are minor memes in the community.