You obviously got a 2 because the instructor felt your performance was substandard in whatever subject that was. I'm sure that during the debrief he must have explained the reasoning behind it. If you wanted to discuss it i would think bringing it up during the debrief would have been appropriate. If done proffesionally then i highly doubt that it would have any chance of reprisals. The guys i've run into are not interested in failing you unless you show them something they really don't like.
I'm sure a quick talk with the instructor in question woukld clear things up. You still may not like his reasons, but at least you'd know why.