How to account for big gap between scores of course work of the first two years and scores of the comprehensive exams ? My comprehensive exams failed recently because of  lower scores "D" in the written examinations of three fields( one major field and two minor fields). 

When Graduate Chair conveyed the result to me at the meeting, I asked her why scores of course work in the first years are good, GPA 3.5, whereas scores of the comprehensive exams are so low despites the fact that the course work and the comprehensive exams are the same professors and the same requirements whereas I had been diligent and complied with instructions of faculty, reading, writing papers, step by step moved towards the coming of the comprehensive exams. 
 Graduate Chair replied that the standards between the two are different, is it reasonable?
In my experience, it's not uncommon to have qualifying exams that are more difficult than passing graduate level courses in the same subjects. 

My advice to students is that we fully expect students to know more to pass the qualifying exam than to get an A or a B in the course.  For example, multiple textbooks are included in the qualifying exam syllabus, and students are expected to be familiar with the material in all of those books rather than just the one textbook that was used in the course.  

In the exams that I'm involved in, as a rule of thumb, I tell students who got an A in the course that they'll need to put in a substantial effort (a couple of months) to prepare for the qualifying exam.  For students who didn't earn a solid A in the course, even more preparation will be required. 

How common this is at other universities really doesn't matter, since you need to pass the exams as they are given at your institution.