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.
Anyway, it doesn't have to be bots... maybe some 3rd-party client app is implementing the downvoting of submissions via (unofficial) API calls.
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.