The best way to respond is to look over your comment to see if it broke the site guidelines in any way (https://news.ycombinator.com/newsguidelines.html). If you notice something, you can correct it in future comments; if you don't, chalk it up to the internet being weird; and either way, don't sweat the downvotes.

Also, if the downvote was weird, someone else will usually come along and add a corrective upvote (https://hn.algolia.com/?dateRange=all&page=0&prefix=true&sor...).