Luckily, short fiction is easier, in some ways, than long fiction. In the beginning, you must hook the reader; you must set up the story problem. In the middle, you must make things worse for the protagonist(s). The story problem gets even more dire. Also in the middle, you must set up the protagonists with the tools to succeed--even as it looks like they will fail. Piece of cake, right? Ha!
How you do this is totally up to you. If you have to write a muddle and then rewrite it, so be it. I have personally rewritten many a muddle. Having some one else read your work may help you identify muddles. "What happened here, in the middle?" Please don't send us your muddle. :)
Good luck with your middles!
In other news, the deadline for the awesome August 2014 issue of Electric Spec is approaching. Submissions need to be in by July 15 for consideration. Thanks!