So obviously link building is encouraged as long as it is natural, organic and has meaningful links with content relevant to your site. Obviously with the constant release of new updates to algorithms, Google is flagging sites for unnatural links to their sites.

My Question is:

• Can this be caused by templating systems? With WordPress for example, where you can add a link on the footer and it is repeated throughout the entire website generating thousands of links?
• If we don't add any links, Good Content will be re-posted and linked to, surely if your content is constantly linked to this will flag your site for "unnatural" content as it's difficult to see if someone has been paid to write an article on your content.
• Or does Google just simply want us to audit some of the links to show we are making an effort?

As you can tell we have had a Manual action for: Unnatural links to your site—impacts links. However, this seems to impact our website as well.

Edit:

To clarify the question:

Can you get penalised for paying for advertising on a site that uses a templated sidebar. So when they create a new blog/page ect your link is also added onto the page hence resulting in 1000's of links to one page on our site. I know that one effect maybe a 0 pagerank web page linking to your page dilutes the PR of our page. However the links are only inbound not reciprocal