One of the biggest disadvantages to using the case study method has to do with external vs. internal validity. Using the case study method, the PhD researcher often does not have control over certain variables and events and, therefore, cannot control them as the researcher could in a lab experiment. Consequently, the researcher using the case study method must be content that his/her findings may only be applicable to similar cases. What the case study gains in internal validity, it loses in external validity.
Many researchers using the case study method make the mistake of relying too heavily on interpretation to guide findings and recommendations. Essentially the researcher becomes part of the research itself and, knowing the expected results, may unknowingly guide the subjects to those results, thereby confirming the expected results. This is known as the self-fulfilling prophecy or Pygmalion effect.
Finally, some members of the scientific community frown upon the case study method because researchers using it often violate the principle of falsification. In modern post-positivist scientific thought (Popper, 1959), the researcher takes the role of the disinterested observer; he/she has no vested interest in whether the research turns out one way or the other (Guba & Lincoln, 1994).
Just like any research method, the case study has advantages and disadvantages for the PhD researcher. If you are thinking of using a case study design for your dissertation or thesis, consider carefully whether it truly captures what you are trying to achieve with your research. Do not blindly choose the case study method because it fits your criteria as the method that you are most comfortable using.