If an author creates a a story where the main plot is a character wants to have sex with family members, shouldn't the story be listed in the incest category even if the main character using sci fi or mind control?
I'd say yes. This is especially important classification in regards to discussions about a stricter sister site.
No. Categories aren't enforced at all. You are free to select any category for any story, no matter what. If incestuous content needs to be marked in the future for filtering/moderation purposes, I imagine it would be a separate system from categories. Otherwise, the incest category would suddenly become the biggest category by an enormous margin. The current category system is also subject to change in the future, which might allow stories to be in the incest category in addition to other categories.
There's probably a larger question here about "ranking" the categories by how niche the fetish, perhaps.
Personally, I'd say you should pick the dominant category or the category with the most focus in the story. Regarding @wicker 's Sci-Fi Incest story example: If the main focus is Incest and the catalyst, setting, or means of incest is sci-fi or mind control related then I'd say Incest should be the chosen category. If Sci-Fi or Mind Control is the focus and incest happens along the way, then SF or MC should be the chosen category. Though I agree with @insertnamehere in that you can select any category or take your pick if you feel one will generate more interest or if the multiple categories have equal or similar weight. But as a courtesy to the readers, an author should probably indicate any secondary categories (from the main category list) that are also dominant in the story in either the subtitle, description, or author's note and not just toss it/them into a wall of tags. TL;DR: The sci-fi, incest, BSDM, group sex, mind control story should be clear before the reader begins the story. The ultimate category choice is debatable, based on the story and its focus.
I'd say yes, it should be tagged as incest. I write incest stories that frequently are mixed with other themes such as MILF and BDSM. But incest can be a major turn off and a trigger for some people so out of respect I'll always tag my stories as incest.