A while back, I took a course that involved gothic, detective / mystery and horror fiction. It was not a writing course, but rather a comparitive literature course. And it changed the way I think about building plots, especially in short fiction.
For the detective side of the course, it focused on the cultural evolution that made the form so popular in its infancy, on the use of the scientific method as a framework for detective work, and most importantly, on the rules of fair play.
Fair play covers both how the crime is committed - it needs to be plausible; it can't be a random accident ... and in a "real world" story, the supernatural can't be involved - and how clues are provided. It also covers how the detective solves the crime, which means that leaps of intuition and stumbling upon answers by luck is usually out.
Fair play boils down to a set of rules for allowing the reader to play along and essentially "race" the detective to the solution ... and I've found that fair play applies to far more than just the conventional mystery story, though it's eminently useful there. It can be applied to any story where the outcome involves a surprise, revelation or a solution not apparent from the opening.
Have a character who is a traitor? Play fair with the how, the why and the foreshadowing. For me, "playing fair" with my reader is far more important than surprising them with a twist ... though for the stories I've done this where I've had them critiqued, a satisfying number of people don't pick it up ahead of time but definitely can read back into the clues.
Have a plot that hinges on a power the character has? You can't just trot it out in the last page. (I did extended foreshadowing on something like this with "The King's Passing" - which IS a mystery story, but the character's supernatural ability isn't at all part of the mystery.)
Need a character to overcome great odds? They can't be bailed out by a god or a benevolent stranger at the last minute.
To me, I think most short stories are their own kind of mystery. They pose a question, the answer to which is initially concealed, and revealed throughout the plot. Certainly, you couldn't categorize most shorts as mysteries in the classical sense, but I've found thinking about them that way when building helps me with structure and even micro details.