As far as I know, the reason is historical; way back in the day fiction was either mundane, set in the "real world", or "fantastical", which was SF or Fantasy. More, Fantasy didn't bloom as a separate commercial genre until the 70's; most SF imprints mixed fantasy in without much concern.
Today the issue is the opposite; instead of SF and Fantasy being ghetto-ized, their more common tropes and themes are routinely appropriated in "watered down" or "bastardized" form for other "Genres". (Romance, youth, Young Adult, mystery, military action, etc).
Shouldn't matter: the classifications are fuzzy to start with and they mostly exist for marketting purposes anyway.
Still, it does matter to many.
(Me, I'm very mildly peeved at perfectly fine SF tropes and stories getting dumped into "paranormal", which I grew up associating with ghosts, monsters, and crackpot theories ala Von Daniken.
)