I use hckrnews myself and don't see this happening. Would you mind identifying which threads you think have been incorrectly flagged?
So in that respect, I often agree with the submissions that get flagged (including this one), but I do think news.ycombinator.com could do a better job of collecting and displaying these flagged submissions. For example, duplicate submissions could be made children of the submission that was allowed to stay.
The biggest gripe I have with the flagging is the paternalistic aspect.