FWIW, looking at my flagged history, I can only presume that in 2012 I thought "flag" meant "mark as important / put it in my favorites" (similar to the little flag icon you could put on email messages back in whatever email client I had used decades earlier).
Not sure what is controversial about the Great Oxygenation Event. Some submissions are auto-flagged for any reason like having astroturfing history, some people don't like the source (I flag a lot of The Register articles as it's a low quality tech tabloid prone to posting manipulative flamebait, in my opinion), some people think it's against the HN guidelines or not front-page-worthy for any reason.
Where do I go to downvote stories?
He’s mistaken. Not all people can down vote. I’m not totally sure of the criteria, I believe it’s old timers or karma points related
pretty sure it's only comments you get the ability to downvote once reaching a certain threshold. Stories you can flag or upvote, but I've never seen a downvote for them.
For comments yes, but can anyone actually downvote stories?