Asking for weaknesses tends to put the referencer on the defensive, as if he or she is sharing something illicit. Instead, I ask the referencer the question below. Everyone has strengths and weaknesses. And most jobs require teamwork. The best team members complement each other’s weaknesses. This is an indirect path at reaching the same answer. It doesn’t always work, but it’s my preferred route. I spend the most time of the interview on this question:
What kinds of people does the referenced need around him/her to be successful?
(1) Cf. Hanan Lifshitz’ approach: “After conducting dozens of reference checks filled with over-optimism, I found the best way for breaking through the praise is to say: “Listen, none of us are perfect; I have weaknesses, you have weaknesses, everyone has weaknesses… Now, what are John’s weaknesses?” At that point the truth almost always comes out.”
(2) Cf. Scott Cook’s method for finding out about someone’s weaknesses — see How do to reference checks: Scott Cook.