People with enough positive points have the ability to flag a comment or submission to indicate they don't feel like it belongs. Why it's flagged is sometimes difficult to figure out.

Here's the FAQ entry

https://news.ycombinator.com/newsfaq.html

What does [flagged] mean?

Users flagged the post as breaking the guidelines or otherwise not belonging on HN.

Moderators sometimes also add [flagged] (though not usually on submissions), and sometimes turn flags off when they are unfair.