A Google Webmaster Help thread has Googler John Mueller saying that when Google has to ignore links on your site, it can lead Google to having to work harder to understand your web site.
As many of you know, a link penalty is not always a penalty. Often, instead of Google downgrading your web site for having bad links to your web site - Google will instead ignore links that they feel should not be counted. That might feel like a link penalty because your rankings may drop when Google does that but it is not like Google is giving you a negative penalty due to links.
That being said, Google's John Mueller said that when Google has to ignore your links it may confuse Google's algorithms in figuring out what your site is all about.
What's happening here is that we're ignoring some of the links pointing to your website, which on the one hand can be useful if these are problematic links that you don't want to have counted, but on the other hand, it would be easier for our algorithms to understand your site if that wasn't necessary. Past those ignored links, there is no manual action being taken against your website, there is no penalty involved.
Am I looking into his words too much or is there something here?
If you think about it, Google is ignoring part of your linkages and clearly that can make things more confusing.
Forum discussion at Google Webmaster Help.
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