I believe HN's algorithm tends to relatively downrank stories with a high comment-to-upvote ratio, because they are more often flamewars on divisive topics.

Another major algorithmic down-ranker is vote wars on comments.

If lots of people are upvoting and downvoting the same comments, that's treated as a signal the topic is contentious and people are likely to start behaving badly.

HN is very clear they prioritize good behavior as the long term goal, and they are as a result comfortable having contentious topics fall in the ranking even if everyone involved in the discussion feels the topic is important.