The middle of a story is undoubtedly the hardest part to write because here is where you have to keep the reader's attention alive so that he will keep on reading to the end. Many writers begin with a great idea, write the beginning and know what the ending will be, but don't plump up their middles enough and so the reader loses interest.
With short stories in particular it's where you have to keep the story tight and not let it wander off into obscurity. If this happens though and you feel the middle is lacking something and can't figure out what, try dividing the story into three sections and work on them individually. Often it helps to focus on one part at a time, especially if it's a fairly long short story.
In novel writing, the middle is where a book can lag or become boring, and of course you must never let that happen, your main job as a writer is to keep your reader turning the pages. If you have this problem it can help to work on random chapters, rather than working chronologically. Strengthening each chapter so that it stands alone means that you will strengthen the whole book. You can always ensure a good flow from chapter to chapter later once you have firmed up the foundations.
In conclusion: sometimes you need to try various ways of writing to get you through a rough patch. Don't be afraid to experiment a little until you know which method works best for you.