What is the difference between Manual Actions and Google Penguin Penalties?
Google Penguin is an algorithmic Penalty (also referred to as a ‘Filter’) while the ‘Unnatural link warning’ (as it used to be called in 2012) is a manual Penalty. In the first case, your website triggered the Google algorithm and was thus penalized. In the latter case, an actual human from the Google Webspam team has reviewed your site and issued a manual action. Google will inform you about a manual action, but not about an algorithmic Penalty. To remove a manual action, you can send in a Reconsideration Request via your Google Webmaster Tools account. Algorithmic Google Penguin filters do not give you the option to file a Reconsideration Request with Google.
Both Penalties are based on bad, spammy and low-quality links, and require you to clean up your backlink profile. Read a summary of 3 different Penalty cases here and learn how they managed to remove it in each case.