Doesn't this pretty much preclude questions about scifi movies being asked on Movies.SE because almost (if not every) question about a scifi movie is by its very nature Science Fiction?
Is Star Wars a movie? Yes - let me post it on Movies.SE.
Oh wait, it's also scifi related... maybe I should post it on SciFi.SE instead?
The average person isn't going to agonize over the decision; they're going to post it on the "wrong" site and have with a lousy user experience when they find out their question has been moved/closed or that there's a battle going on over whether or not they posted it in the right place.
Ditto for Literature.SE / SciFi.SE. Questions about SciFi books are appropriate for both places. What about Superuser + AskUbuntu/Apple.SE? Pretty much anything in AskUbuntu is appropriate for Superuser as well as any Mac questions under Apple.SE.
IT Security / ServerFault?
Statistical Analysis / Mathematics?
Theoretical Physics / Physics?
Major potential for overlap has been created as StackExchange has been expanding and it's only going to get worse. If questions are appropriate for multiple sites, then their asking needs to be facilitated.
Why not create some kind of association between overlapping sites where the "Questions with similar titles" that appear when the title for a question is entered can be expanded to search other sites that will overlap? This way, if anyone tries to ask a question on SciFi.SE that may already exist on Movies.SE or Literature.SE, they'll appear in the results and hopefully prevent the duplicate from being asked.
Edit: They should appear in general search results too.