A deleted post-credit scene from the first Iron Man film confirms mutants exist in the Marvel Cinematic Universe.
Kevin Feige revealed the deleted scene saying, “We have a vault and we pulled some thing out of that vault that we said, ‘We’ll never show this to anybody. Put it away.’ We’re bringing them out. We’re putting them on this disc and I’m about to show you a deleted scene that has never been seen by anyone before right now. Thank you again so much and enjoy.”
The scene is an alternate post-credit scene of Samuel L. Jackson’s Nick Fury revealing the Avengers Initiative to Tony Stark.
Jackson’s Fury says, “As if gamma accidents, radioactive bug bites, and assorted mutants weren’t enough. I have to deal with a spoiled brat who doesn’t play well with others and wants to keep all his toys to himself.” Stark asks, “Who the hell are you?” Fury responds, “Nick Fury, director of S.H.I.E.L.D., I’m here to talk you about the Avengers Initiative.” Stark asks, “Well, what are we avenging?” Fury responds, “Whatever the hell we want.”
At the Saturn Awards, Kevin Feige revealed an alternate version of the post-credits scene from ‘IRON MAN’ with Nick Fury mentioning “mutants” and “radioactive bug bites”. It will be included in the upcoming INFINITY SAGA boxset. (Source: @BRMarvelNews ) pic.twitter.com/AqzTokEc67 
— DiscussingFilm (@DiscussingFilm) September 14, 2019 
The original cinematic post-credit scene removes the reference to gamma accidents, radioactive bug bites, and mutants. Fury says, “I am Iron Man. You think you are the only superhero in the world? Mr. Stark, you’ve become part of a bigger universe. You just don’t know it yet.” Stark asks, “Who the hell are you?” Fury responds,” Nick Fury, director of S.H.I.E.L.D., I’m here to talk to you about the Avenger Initiative.”
The reference to mutants in this now revealed post-credit scene will fuel theories that the mutants have been around in the Marvel Cinematic Universe from the beginning. In fact, a number of people speculate the SR-71 Blackbird shown during Tony Stark’s Iron Man Mark II test flight is a direct reference to the X-Men.
The X-Men’s iconic aircraft that was introduced in 1975 is titled the Blackbird. The name is an obvious homage to Lockheed Martin’s Sr-71 Blackbird. However, it had a different look when it first debuted in the comics.
However, in the recent X-Men films the plane looks almost identical to an SR-71 Blackbird