Unfortunately, this is not a problem with K2 but with Joomla! 3.0. The "canonical" meta tag is reporting the wrong URL for items and it's what Facebook or other social networks obviously put more weight too if your site doesn't utilize their meta tags.

Upgrade to K2 v2.6.5 to trick Facebook for now (as we use the ogp:something meta tags).

But Google won't like that either way.

A quick solution is to kill this meta entirely until it's fixed on Joomla! 3.0.

E.g.
$document = JFactory::getDocument();
unset($document->_links);

at the very top of your template's index.php file (inside a php block obviously)

See this page for example:
egnatia-post.gr/index.php/world/item/2022-%CE%B7-%CE%BC%CE%B1%CF%84%CF%89%CE%BC%CE%AD%CE%BD%CE%B7-%CE%B5%CF%80%CE%AD%CF%84%CE%B5%CE%B9%CE%BF%CF%82-%CF%84%CE%B7%CF%82-%CE%B1%CF%81%CE%B1%CE%B2%CE%B9%CE%BA%CE%AE%CF%82-%CE%AC%CE%BD%CE%BF%CE%B9%CE%BE%CE%B7%CF%82

and notice the meta tag:
<link href="egnatia-post.gr/index.php/world" rel="canonical" />