What are the likely causes of death when an autopsy is inconclusive?

Often we read news stories where an autopsy on relatively fresh and unmutilated the body of an alleged murder victim is inconclusive as to the cause of death. What are the likely causes of death when such an autopsy is inconclusive? Are autopsies actually that hard or is the inconclusive finding a more political thing than a medial truth? If not, what medical causes of death are so hard to identify? For example the Kelli Lynn Murphy case.