I just found this little nugget whilst search for something completely unrelated. #2 Post from Google employee: [google.com...]
That's pretty clear admission they are hitting sites they don't mean to imo.
That particular Googler (Pierre Far) has been posting here recently [webmasterworld.com], too - usually very helpful and clarifying contributions.
Yes, Google's algorithms have always made false positives (sometimes they also get called "edge cases, I think). I've always appreciated their willingness to publicly admit this, and to correct the problems they learn about - even for the "little guy."