Is there any way to learn for sure why Google penalized a specific site? I think about situation when webmaster/site administrator is aware about Google rules and is sure they aren't breaking any, but the site is penalized nevertheless.

The only information you get from Google is that they processed your reconsideration request but they neither say what is the result nor what is the penalty reason if they keep the site penalized.

You can try to get information on Google webmasters forum or here but most of the time these are only speculations.

Considering the site administrator tried to find out what's wrong but failed, is there a source which can tell what is the problem?