When Wolverine is first in your party and goes up against Frank West (Dead Rising), Wolverine will say "Me and Guys named Frank don't get along so well..." this is a reference to Frank Castle, A.K.A. "The Punisher". Wolverine and The Punisher have a long running distaste toward one another.

Magento will reference his son, Quicksilver, when he wins a fight against Dante. "Brash, arrogant, rude, even a white head of hair... You remind me of my son in many ways."

The Ancient Warrior DLC skin set was supposed to include a new skin for Magneto. This skin was taken from the Marvel event "House of M" where Magneto's daughter the Scarlet Witch changed the entire world. The skin generated controversy because it looked like King Juan Carlos of Spain.

Unlike Strider Hiryu and Mega Man characters, Arthur does not have a death animation that mirrors his original death animation, in which he becomes a pile of bones. However, he will become a skeleton in his DLC costume when his powered-up armor shatters.

When you defeat Dante (Devil May Cry) as Deadpool, he'll say, "Next time, maybe you should let Nero do your fightin' Skippy." This is a reference to Devil May Cry 4, where Nero was the main character for the majority of the game.

When you defeat Arthur (Ghost n' Goblin's) as Deadpool, his victory quote will say, "And THAT'S for lulling me into great side-scrolling adventures that were never possible to beat!" This is a reference to how the old NES game, "Ghost n' Goblins" is considered one of the hardest games in history, due to its high level of difficulty and the fact you must play through the game twice in order to achieve the 'good' ending.

When Deadpool is first in your party and goes up against Spider-Man, he says, "Gonna rough you up like a Broadway musical." This is a reference to the Spider-Man Broadway musical accidents, in which actors portraying Spider-Man from the critically disliked late 2000s musicals often fell from the faulty stunt ropes during a particular scene, resulting in serious injuries and medical attention. After defeating Spider-Man,he will say, "Aw, that was too easy! Maybe it would have helped if you'd turned off the dark!", referencing the musical again.

Even though Deadpool is damaged by Ghost Rider's Penance Stare due to gameplay mechanics, in the comics all he saw was a "highlight" reel (e.g. what led to him becoming what he was) and changed Ghost Rider back into Johnny Blaze.

If you enter the battle in Deadpool's alternative outfit, "Cablepool", Deadpool will say "And you thought Cable wasn't in this game..." This is a refrence to Cable being in Marvel Vs. Capcom 2, but not returning to Marvel Vs. Capcom 3.

When Deadpool is first in your party and goes up against Magneto, he'll shout, "HAHAHA! Magneto! Welcome to die!" This is a reference to the 1992 X-Men Arcade game, where Magneto had 2 infamous mistranslated lines, "I am Magneto, master of magnet!", and "Welcome to die!"

According to Ryota Niitsuma, producer of Ultimate Marvel Vs. Capcom 3, this game was released as a stand-alone disk instead of DLC because the earthquake and tsunami that hit Japan threw off their development schedule.

Haggar's Double Lariat costs a small amount of health to use, a nod to how it operated in his original franchise, Final Fight. As a tradeoff, attacks will completely miss him during most of the animation.

The mechanics of C. Viper's moveset are based on her debut in Street Fighter IV: her EX Moves cost meter, and she retains the Focus Attack technique available to all fighters in Street Fighter IV.

Zero's moveset has at least one move from every game he was playable in from the Mega Man X series.

• The Z-Buster is from Mega Man X3
• Hienkyaku, Ryuenjin, Shippuga, and Kūenzan are from Mega Man X4
• Sougenmu and Genmu Zero are from Mega Man X5
• Sentsuizan, and Rekkoha are from Mega Man X6
• Hadangeki is from Mega Man X7
• Raikousen is from Mega Man X8

Several characters mention Mundus, the main antagonist of Devil May Cry, before or after fighting one of the characters from that series. Before the battle with Trish, Ghost Rider will say "I eat demons like Mundus for breakfast.". Phoenix (Jean Grey), after defeating Vergil, will say "Perhaps if I'm not too busy, I'll take care of Mundus, too." Dormammu also says to Dante that he should stick to fighting Mundus, implying not only that Dante is not strong enough to defeat him, but that Dormammu is more powerful than Mundus.

Dante's appearance, as well as his moveset, are based on his portrayal in Devil May Cry 3: Dante's Awakening. The only new moves are Million Dollars, Devil Must Die, Bold Move and Weasel Shot.

Although Jill and Sentinel classify Deadpool as a mutant during their pre-fight dialogue, he technically isn't one. His powers are a result of the Weapon X project, rather than his genes, making him a "mutated human" or "mutate", rather than a "mutant".

When Iron Man wears his alternate costume "Iron Patriot", his intro line sometimes changes to him muttering "Ugh, I can still smell Norman Osborn's hair gel." This is a reference to the Patriot Suit being designed and used primarily by Osborn during his time as leader of HAMMER.

Nemesis was confirmed not to appear in the original Marvel vs. Capcom 3 release due to being deemed "too gruesome", with risk of changing the game's rating. Capcom reworked Nemesis' animations to make him work within a T rated game.

There was a discrepancy in Phoenix Wright's level 3 Hyper Combo. When dealing the final blow, he would say "Take this!", while his speech bubble displays "Take that!". This was later fixed in the Heroes and Heralds patch.