Most problems encountered when modeling are the result of applying a rational act in an unanticipated way. For example, extruding a 2D shape in a positive axial direction ("up" for example) may produce different results from extruding the same shape in a negative axial direction ("down"). Others result from applying tools without fully considering the implications. Others arise from outright programming errors on the part of those that made the software, or a misunderstanding of the tools on your part.
Obviously, some problems cannot be addressed by a resource such as this. However, there are some fairly common "issues" or "considerations" which may apply. Knowledge and consideration of these issues may help you avoid problems.
Last updated: April, 2014