1. First of all, make sure that their story flows.  Some students have a tendency to try to put steps in that do not fit in the events of the story.  The clues they used to lead you to the conclusion should naturally occur.  If students are having difficulty, they may require reading some examples, or some one-on-one tutoring.  If often find that if students think of it in terms of a movie, they are more likely to understand that the order of events they have created do not make sense and they need to reevaluate some of their ideas.
2. They may also have difficulty with changing scenes too frequently.  Because a mystery is rarely, if ever, solved the same day or the day after, they like to have several scenes and several days throughout the course of the story.  This can lead to a story that is very choppy and can confuse the reader.  In this case, I find that it is also good to encourage them to try to condense the number of scenes.  You may even want to establish that the story needs to take place in      places and no more.  By limiting the number of settings, you may eliminate that problem.  It is more important simply that you are aware of the changes happening in the story and that those changes do not detract from the quality of the story.