The films pull more from the Ultimate line of Marvel than the actual true continuity, though there are elements from there, as well. (The Ultimates line is an updated and reimagined 'Marvel world', though not the true one.) That's why you see a black Nick Fury in the films, the Avengers working with/for SHIELD and all the blatant mistakes in the X-men films as per membership/seniority.
Beyond that though, the Marvel films suffer from the same thing that all films which are made from existing literary material - the people making them always think they know better than the original writers and can't resist mucking ahem changing things up. ;)