While it might make syntactical or logical sense to answer the question with "Yes," that's simply not how anybody ever does reply to it.
Illogically, "No" is the normal response to both:
Have you seen this movie?
Haven't you seen this movie?
This is one of those cases (there are actually many of them) where the English language takes a detour from common sense and falls back on actual usage.
Another way of answering the question, which actually makes sense, is simply:
If you don't want to say something that seems off, you can reply in that fashion. It may sound be a bit more formal, but it's still quite acceptable.
Other possible answers, which also make sense but are much less common and sound slightly awkward, include:
That's correct, I haven't.
That's right, I haven't.
Normally, those would be given in response to a statement (you haven't seen this movie) rather than a question.