Without specific links it's hard to tell, but there are some automatic rules that often kick in in cases like this. The penalty I notice most often is the comments-vs-points ratio. If people just keep adding comments without voting for the article itself, the link gets penalty and may lose quite a few positions.

Whether you want to call that censorship is up to you, but there are a few projects which attempted reverse engineering of the HN sort order and the features were primarily automatic. What I'm trying to say is: what influences the positions is usually the nature of the discussion rather than the content. Can't prove it for every case though.