When you don't understand something that someone is telling you or need clarification don't ask, "Why?" (e.g., "Why did you think that?"  "Why did you do that?").

A "Why" question tends to makes people feel defensive because it appears to question their motives.  You can, however, ask essentially the same question without receiving a negative/defensive reaction if you just phrase it in a slightly different way.  For example:  What stopped you?  What got in your way?   What caused you to react that way?   These types of questions appear to point outward to external factors that are easier for people to discuss.