The [flagged] marker shows up on a post when there are enough flags to kill an item. Whether it's actually killed or not depends on that and a few other things, such as how active the discussion is. That's why https://news.ycombinator.com/item?id=27030269 shows [flagged] but not [dead].
But flags affect the ranking of a story long before they reach that fatal threshold. That's the case here. Moderators haven't done anything.