The Most Glaring Unexplained Plot Holes In Marvel Movies

In Iron Man 3, the Extremis solution can regrow limbs and heal human tissue from nearly any injury. So why hasn't Tony looked into that? It saves Pepper Potts, for crying out loud!

Instead of burying it in the archives, why not perfect it and use it to help heal his allies? Surely a man who can synthesize his own elements can perfect this new breakthrough and use it for the good of all mankind.

Agent Coulson's death in The Avengers helped bring the team together, but now that Coulson is alive, do the Avengers know? Joss Whedon, director of The Avengers and Avengers: Age of Ultron and creator of Agents of S.H.I.E.L.D., considers Coulson to be dead in the movies. But in the show, Coulson's revival is supposedly kept secret from Thor the Avengers. How is that possible?

In S.H.I.E.L.D., Coulson carries out missions with Thor's Asgardian friend Sif, so does she keep that a secret from Thor? After Coulson clears undercover Hydra agents from S.H.I.E.L.D., how do Black Widow, Hawkeye, and Cap not know about him?

So Thanos's big goal is to collect all the Infinity Stones to achieve godlike power, right? But he needs help collecting the Tesseract AKA the Space Stone from Earth. So he gives Loki a powerful scepter that contains one of the stones to retrieve it. Why would Thanos do that?

If he's trying to collect and protect the stones, why would he risk unnecessarily losing one to gain another? In fact, he does lose it! The Mind Stone he gives to Loki ends up embedded in Vision's forehead. So now he has to recover that stone and the Tesseract. For an intergalactic tyrant, he sure isn't that smart.

In Iron Man 2, Tony Stark discovers a way to synthesize a new element to use in an overhauled arc reactor, replacing the palladium that is poisoning him. This may be vibranium, though some movie fans claim otherwise.

If Stark made an entirely new element, he'd still have the means to access it. Tony's father Howard Stark found enough vibranium to make Captain America's shield and Tony was aware of Ulysses Klaw's smuggling of the stuff from his arms-dealing days. So if Tony knows how powerful vibranium is, why doesn't he make at least one indestructible suit out of it?

So the world is attacked by aliens in The Avengers and not one government calls for an intergalactic military plan? Even S.H.I.E.L.D. is preoccupied, battling with Hydra and other Earth-based threats instead of preparing for more alien ones. Did anyone at least do an exploratory autopsy of one of the several thousand Chitauri corpses lying around New York City?

The only person on Earth who is concerned about protecting the world from alien threats is Tony Stark, who suffers from serious PTSD after nuking an alien army and falling through an interstellar wormhole.