So you've managed to beat the odds. You're in the second-look pile and I'm going over your story like a drug sniffing dog looking for weaknesses to decide who gets published and who gets a disappointing rejection email. Here's what I look for:
1) Don't put action in your dialogue tags. I'm going to say you can get away with this once or maaaaybe twice in the space of a 2500-5000 word short story, but not more. It stands out too much. Here's an example:
"Oh, my goodness," says Janey, as she stands and puts the flowers in her hair.
Do this instead: "Oh, my goodness," says Janey. She stands and puts the flowers in her hair.
2) Make sure your verb tenses match. If you're writing a story in past tense that suddenly switches verb tenses in a secondary phrase, it slows down my eye and weakens the prose. Observe:
"Here are some flowers, my love," David said. It was four in the afternoon and the sun hung heavy against the horizon.
"Oh, my goodness," said Janey, standing up and putting the flowers in her hair.
Do this instead: "Oh, my goodness," said Janey. She stood and put the flowers in her hair. Not only did we eliminate that pesky dialogue tag run-on, but we also now have nice, smooth, agreeable verbs.
3) Don't overuse or misuse Em dashes. We know "(insert trendy beloved author here)" uses them like a Get Out of Semicolon Free card to tack random phrases onto the end of sentences but, as The Slate and Philip B. Corbett point out, this is an irritating and amateurish habit to get into. Em dashes can be used unobtrusively as commas in a parenthetical structure--like this--or they can be used like a strong ellipsis to indicate a speaking person being abruptly cut off, but they are not and should not be used interchangeably with semicolons. Once I started seeing these, I couldn't un-see them and seeing them pop up in otherwise good writing is like watching gnats land on my cake frosting.
4) Passive voice and past perfect tense. If you're using Word, just hit CTRL+F and type in "had" and then "were" and also "being". Find all examples of these and if they're being used to modify other verbs, check and make sure you couldn't make that sentence clearer. Sometimes it can't be helped and past-perfect tense creeps its wheezy, clunky way into your story, but realize that these are moments where your story doesn't shine as well as the punchier, faster, smoother ones I see. Be merciless with your prose.
5) Minimize use of the infinitive and rhetorical questions in the narrative or dialogue. I can stand a little of both, but not a lot of either.
6) Don't box your dialogue in. If all your characters ever do is question and answer each other, it makes for really, really dull reading. Declarative sentences or having characters talk but not listen to each other is a hundred times more interesting to me than deliberate or didactic hand-holding in uninspired dialogue.
7) Don't miss the chance to show off. This is speculative fiction! We're like the Sparta of the literary world. We don't just tell Xerxes' messengers to fuck off, we fling them down a bottomless pit. Think of every great speculative fiction story you've ever read. What stuck with you? Names, places, dates? Nah. It's images. Ideas. Set-pieces of epic proportions. Someone did or said something that made you wish you were there. You looked up and saw the sky blotted out by something that you couldn't quite comprehend. Don't miss the chance to exploit this aspect of the genre. It's a big part of what makes science fiction and other speculative stories so persistently popular and entertaining.