Students accepted for graduate study in US institutions are not dumb. If a student is failing the qualifier, you should find out why. A discussion with the student and with the student’s teachers is a necessary part of the process.
Points An Outside Observer Might Raise
Institutions Using Qualification Exams
Should the program chair or counselors be aware of the classroom performance of graduate students before they take the qualifier and arrange appropriate counseling and learning opportunities to insure success?
What kind of counseling was offered to the students after their first failure?
What is the attrition rate for graduate students in this department?
Institutions Not Using Qualification Exams
Are their students less able than yours?
Is the success rate of their students as professional scientists less than the success rate of yours?
This scenario opens up the question of whether a program uses exams to weed people out. Some programs have a reputation for intentionally accepting more students than would pass the qualifier or comprehensive because they needed the TAs.