Bots. I've posted many popular and unpopular takes here. Down always comes first, and as the bot votes evap into the ether, the true human take is almost always revealed after an hour or two.
How this submission got negative votes is the oddity that people are trying to figure out. Regular users can't downvote, and I don't see a reason why it'd be a moderator action for this post, so I'd assume some bug/edge-case in vote handling.
No other /newest submissions (current or that I've previously seen) have negative score. I checked a bunch of your submissions (using https://news.social-protocols.org/stats?id=48104663) and none appear to have ever been negative.
It's possible that this issue was happened to be caused by a bot, but what you're describing as a regular occurrence ("Down always comes first") is probably a misrecollection about comment downvotes rather than submission downvotes - or about reddit which does have submission downvotes.
As stated elsewhere in this discussion: downvotes exist for comments on HN, but not for submissions, as far as anyone is aware, which is what makes it puzzling.