As long as the author or filmmaker has made it clear to the audience that this is a fictional representation rather than history, I don't see why not. A film or a novel is a work of art, and it cannot be thus unless its maker is exaggerating or downplaying or otherwise playing with reality.
Difficulties emerge when a work of art is represented as non-fiction, for example, James Frey's memoir, one he finally admitted contained many untruths. If one is writing about one's own life, or about history, it is definitely not all right to distort the facts. Granted, we all see reality through completely different lens, but we all know, or should know, whether we had lunch with someone or visited our dentist.
Another difficulty emerges when a work of fiction relies heavily on a historical backdrop. For example, The Da Vinci Code ran into controversy because people simply did not understand it was fictional. I am not sure how much more clearly it could have been labeled, and I don't blame the author or the producers of the movie for this. When something is clearly labeled as fictional, it is incumbent upon us to note that. Another example is Gone With the Wind, which probably contains many inaccuracies and exaggerations, but which is probably more responsible for people's knowledge of the Civil War than any textbook they have ever read.
A work of fiction tells a story, a story with a point, one hopes. If "facts" are distorted to make some point about some universal truth, which good fiction is meant to do, if it is clearly labeled, any harm that accrues as a result is the fault of the reader or viewer.