Just got a client whose site dropped from a PR of 3 to zero. This happened shortly after the Penguin release, June, 2012.
Examining the site, I couldn't find any significant duplicate content, and where I did find duplicate content (9%), a closer look revealed that the duplication was totally coincidental (common expressions). Looking deeper, I found no sign of purchased links or linking patterns that would hint at link schemes, no changes to site structure, no change of hosting environment or IP address. I also looked at other factors, too many to mention here, and found no evidence of black hat tactics or techniques.
The site is structured in silos, "services", "about" and "blog". All page titles that fall under services are categorized (silo) under "services", all blog entries are categorized under "blogs", and all pages with company related information are categorized under "about". When exploring the site's links in Site Explorer (SE), I noticed that SE is identifying the "silo" section of links (i.e. services, about, blog, etc.) and labeling it as an anchor text. For example, domain.com/(services)/page-title, where the page title prefix (silo), "/services/", is labeled as an anchor text. The same is true for "blog" and "about". BTW, each silo has its own navigational menu appearing specifically for the content type it represents. Overall, though there's plenty of room for improvement, the site is structured logically.
My question is, if Site Explorer is picking up the silo (services) and identifying it as an anchor text, is Google doing the same? That would mean that out of the 15 types of service offerings, all 15 links would show as having the same exact anchor text (services). Can this type of site structure (silo) hurt a website post Penguin?