You're talking about false negatives, not false positives. People have different tolerances for these kinds of errors.
But yes, I remember that to see that stuff you had to expand the down-modded comments.
That stuff was also a product of its time. Slashdot had the strong free speech ethos of the early internet, so CmdrTaco had a policy of never deleting comments unless they broke the site somehow or there was a legal process requiring it. Sometimes that meant very new stories would get these comments and they'd be visible before they got modded, but if you browsed stories that had been active for a little while you wouldn't see them.
One downside of a sophisticated moderation system on a site designed for programmers is that some people take it as a challenge. The reason Slashdot trolling was a bunch of dumb memes rather than e.g. commercial ads is because a lot of bored teenagers found spamming it a good way to learn web programming. The systematic nature of the moderation meant that it was a system to beat, a game to conquer. Hence the brief influx of "page widening posts" and other technical hacks. But I don't know if you'd see the same stuff today. The culture has changed, there are much better ways to learn programming and way more opportunities now. And you don't have to be fully automated. CmdrTaco had a strongly systems-oriented streak, but the problem on HN is hardly ever the actions of dang and the other paid moderators, it's really abuse of the overly simple system by other users that's a problem. You could have both good paid moderators and stricter controls on user moderation.