If you are wondering why the ranking of your website were affected by Penguin 2.0 update , the frank answer is that your website was involved in unethical means of promoting website, atleast in the eyes of Google.
Google says that any website found violating the Google Webmaster guideline will be punished and by punished they mean degradation in ranking and search results. After May 22 2013, ranking of many websites went down and they disappeared from search results. SEO have been wondering what went wrong. Here is how Penguin 2.0 affected website ranking:
Matt Cutts (Head of Webspam dept. of Google) while announcing the update said that this update will go deeper and later added that it will affect paid linking. 2.3% English searches were affected but bigger was the affect on other languages, which are brimmed with spam websites.
By deeper Matt meant that serious attention to every link will now be given, every page of website will be checked to whether it has quality content or not, spam websites will be punished, unrelated links will be punished, duplicate content will be punished, keyword stuffing will be punished, spam links in forums will be punished, similar match anchor text will be punished. In short every tricks and trades of Black-Hat SEO and Grey-Hat SEO are under scrutiny.
If your websites link building techniques involved paid linking, you need to tell your SEO to stop them and "no follow" the already existing links. Both the website involved in this technique will be affected as Google believes this is an unethical method that deprives audience from fair means of content.
Other technique is to target one or two favorable keyword and use it as anchor text. If your SEO has indexed your website in such a way that you are in serious trouble. Google is not only getting suspicious on websites targeting only one links but is scrapping them fast. You need to take your website offline, change all your Meta tags, spread anchor text, use alternate and different keywords and re-index your sitemap.
Then there is Keyword centric page issues. There are many websites and logs that use keywords as signature or leave them in comment or use them as tag but rest of the pages remains blank. There are many websites that does that, user comes to that page finds nothing, gets frustrated and leaves. Now Google is quickly blocking such pages and as a penalty the ranking of such website, well comes down.