While Marvel was developing The Avengers, they were working on collaborating with the Pentagon on the use of the U.S. military in the film. Ultimately, the Pentagon decided to not support the movie because they were unclear on the relationship between the fictional Strategic Homeland Intervention, Enforcement and Logistics Division, or S.H.I.E.L.D. organization, and the United States. I guess the Defense Department couldn't roll with a movie about a team of superheroes fighting off an alien invasion.
Defense Department’s Hollywood liaison Phil Strub revealed their confusion to Wired,
We couldn’t reconcile the unreality of this international organization and our place in it. To whom did S.H.I.E.L.D. answer? Did we work for S.H.I.E.L.D.? We hit that roadblock and decided we couldn’t do anything with the film.... It just got to the point where it didn’t make any sense.
I don't know about you but I actually find that reasoning absolutely hilarious! I don't see what's so difficult about it, as long as they answer to the President of the United States. That should show you where S.H.I.E.L.D. stands, and in the comics they do answer to the President.
Usually the Military has no issues helping out with making movies, but according to Wired, "the ambiguity around what exactly S.H.I.E.L.D. is provides a vexing complication. If it’s an American governmental agency, what kind of constitutional authority does it exercise over the military? If it’s an international body, as the movie text suggests and Strub determined, are U.S. military personnel and equipment on loan to it through some kind of United Nations Security Council resolution? The questions may seem picayune, but they’re precisely the stuff that can cause an image-conscious military to yank its cooperation from a movie."
Are you confused about where S.H.I.E.L.D. falls in military command structure? Should it even matter? It's a fictional organization for cryin' out loud!