The spam filter influences the number of times a comment needs to be flagged before it becomes [flagged] and gets killed, but if it says [flagged], someone used the "flag" button at least once. Sometimes just downvoting a spam comment is enough to kill it; those just get marked [dead] and not [flagged].
This is a green account where someone used the "flag" button to kill it: https://news.ycombinator.com/item?id=48262928
Note how the former only says [dead] while the latter is [flagged] [dead].