The flame war detector doesn't flag the post (users do), but it does downrank them. You can see it in "hot" discussions. Say they go from 20 to 100 comments in

The flame war detector doesn't flag the post (users do), but it does downrank them. You can see it in "hot" discussions. Say they go from 20 to 100 comments in minutes, mostly with deeply nested chats consisting of 2-3 people in a back and forth. The submission will fall off the front page quickly, but not be marked flagged unless users flagged it.