How to respond to personal/self-deprecating comments by strangers?

Once, during a fine arts class's icebreaker, I was paired with someone and he made a comment about how he was short. Without thinking, I laughed.

I feel like I sort of dragged him into it. I'm also short, and we were doing speed portraits, and I could barely see his face above our back-to-back aisles. I was trying to sit straighter, making an offhand comment about myself, and that's when that exchange happened. It was sort of an awkward rather than mean laugh; I didn't understand how to respond to something to that at the time. Saying something like "no, no" might sound patronizing and disingenuous. At the time I thought nothing of it, because he was still smiling, but he never showed up in that course again. I had no opportunity to apologize once I thought it through.

I'd love it if I could think through interactions more, but some things are just so unexpected, and I can be ridiculously socially awkward. I also know that guys can be insecure about being short, and that it also places them at a social disadvantage, so I felt guilty for a long time. I don't care about guys' heights, but proving that isn't going to help. Instead, I'd like advice on how to respond to self-deprecating/personal topics like these from strangers.