Most story problems occur across all sorts of fiction, but a few of them are specific to particular types of fiction. Writers of historical fiction and historical romance, for example, have the “Tiffany Problem” –that is, the necessity of coping with a historical detail that nobody is going to believe, such as the fact that “Tiffany” is, in fact, an in-period medieval name.†
Writers of science fiction and fantasy, for their part, have problems even at the basic-building-blocks level. If you’re working in that field, your difficulties start right at the beginning of the job, when you have to declare, at least to yourself, the genre of your novel — is it science fiction or is it fantasy? The two may be shelved together in the bookstore, and may share an overlap in writers and audiences, but they nevertheless have different reader expectations and slightly different reading protocols. You therefore need to signal to your readers which genre you’re primarily working in for a particular book.
Published works signal to their audience in multiple ways — the cover art and the cover copy; the advance publicity and the in-store placement; even the choice of who blurbs the novel or who gets an advance copy for review. But a manuscript out on submission goes to the publisher without benefit of any of that stuff; the writer needs to embed the signals in the text itself. What this means is that you need to be clear in your own mind which side of the sf/fantasy divide your story is on, and you also need to be clear about just how much you want to obscure or reveal your story’s position before the end.
There are in fact some novels in both genres where part of the point of the tale is the ultimate revelation that what appeared to be fantastic is actually science-fictional, or that what appeared to be solidly rational science fiction has actually lured the reader deep into the murky id-forest of the fantastic. But playing that game requires crystal clarity in the writer’s mind about what’s really going on, plus a deft hand with the placing of clues and the pacing of revelation. Once your own mind is settled on the question, then you can punch up the details that point in the desired direction and lower the emphasis on the ones that point the other way.
If you’ve done it right, your readers may feel surprised and they may feel disoriented, but they won’t feel cheated.
†That one’s actually fairly easy. Go with a period spelling, like Tiphaine, or go back to the original Greek Theophania. Problem solved.