The reason these things happen most of the time is cost. Although the Pearl Harbor vs Tora Tora Tora! comparison is fair as Pearl Harbor was garbage movie.
My brother just recently consulted as a historian on a major movie and one thing I learned from him was that even when the writers, directors, and producers want a truly authentic piece, compromises must be made. In the most critical areas in the film they tried to be 100% a pure as possible while in others there are liberties both in the sets and general story.