When Deadpool starts his Level 3 Hyper Combo, he strikes a pose and says "Boop-oop-a-doop". This is a reference to the catchphrase of the classic cartoon character, Betty Boop.
During Ryu's ending, when he is facing off against Iron Fist in a fighting tournament, a board for an upcoming match of Ken versus Mr. X can be seen. It is unknown if this is referring to one of the characters called Mister X from Marvel's universe or Mr. X, the T-103 Tyrant from Resident Evil 2. None of these possible characters, in addition to Ken, are playable in the game.
Instead of using Iron Man's original theme from Marvel Super Heroes or writing a new one, they used a dance remix of War Machine's theme from Marvel vs. Capcom: Clash of Super Heroes.
Sentinel's character bio specifies his serial number as COTA-94. This is a reference to Children of the Atom; the first Capcom fighting game to feature X-Men characters, released in 1994.
When Deadpool defeats Magneto he says "I just beat Mag-freakin'-neto! Where your curly mustache at?!" This line comes from a video featuring the gameplay and voice of Marvel Vs. Capcom 2 world champion Michael "Yipes" Mendoza, in which he says the same thing.
There is a mistake in Chris Redfield's ending. In the ending, Chris has Albert Wesker on trial with Matthew Murdock (Daredevil) prosecuting. Matthew Murdock was never a prosecutor, as he is a defense attorney.
Dead Rising's Frank West was originally meant to appear in the original Marvel vs. Capcom 3 as a playable character. However, Frank was cut from the game for causing unspecified lag issues. Interestingly enough, it was confirmed that the helicopter pilot Chun-Li was riding into the S.H.I.E.L.D. helicarrier in the second promotion cutscene of the original Marvel Vs. Capcom 3 was Frank West. Frank West's silhoutte can also still be seen in the background of one of the original Marvel Vs. Capcom 3 promotional art pieces. Frank West would later become playable in Ultimate Marvel Vs. Capcom 3.
There is code in the game's data that would suggest that Doctor Octopus would have appeared in the game as a playable character.
Director Ryota Niitsuma has stated that Blade was considered as a playable character for the game, but they decided not to include him as they didn't want too many characters that use swords.