For some reason, I was under the impression that there was one manual action that Google sends out to some webmasters that is a warning of something that looks spammy but no negative manual action was taken on the site.

I was wrong.

Former Googler, who worked in the manual actions team, Kaspar Szymanski, posted on Google+ that any web spam related manual action always impacts part of all of the site in a negative way.

Kaspar said:

I tried to look back at an example of a manual action notification that I thought did not impact the site, but maybe it had to do the the granular penalties we’ve seen?

Kaspar’s advice:

It is very important to take such warnings seriously. They are not sent likely and should be considered a wake up call. If received first thing to do is to take a long, hard look at the site’s backlink profile and compare it against Google Webmaster Guidelines.

Please don’t ignore Webmaster Tools Messages!

Forum discussion at Google+.