There is nothing wrong with a top comment being a contradiction. I believe that in this way, it might bring even more useful comments and thoughts since it takes a different angle.
The real problem is that those contradicting comments usually are plain simple negative (not to be confused with criticism, which is alright, I am referring to the grumpy negative ones), demotivating.
There's nothing wrong with useful critique or argument. But as others have said it's very easy to dash off a very quick rebuttal of a minor point in an article, ignoring the main thrust of whatever the article is about.
When I've read six pages of interesting and useful article it's depressing to see the top voted comment on HN is about a footnote on page 4 with little relevance to anything interesting.
The real problem is that those contradicting comments usually are plain simple negative (not to be confused with criticism, which is alright, I am referring to the grumpy negative ones), demotivating.