Incoming links which don't exists...

[jj3434]

I believe our site is being penalized/held back in rankings, and I think this is why...

We placed an advert on a website which they didn't make "no follow" so we had hundreds of site-wide links coming into our site. We asked them to remove the advert which they did. This was 4 months ago, and the links are still showing in GWMT. We have look into their pages which GWMT is saying still link to us, but these a number pages aren't being indexed by Google, and others aren't being cached.

Is it possible that because Google cant find these pages, it can tell our link has been removed? And/or are we being penalized for this?

Many thanks

[MickEdwards]

As soon as you place a link on a site that is site wide you have to wait potentially months for Google to crawl every page on that site, which is why GWT might still be showing the detail.  GWT is not the decider as to whether Google takes some action.

As long as you have rectified with either a no-follow or removal you are fine and have done the right thing.

[Dr-Pete]

If these are all coming from one site, and you're worried about them, this is actually a good case for the disavow tool. You can disavow an entire domain in a single line:

https://support.google.com/webmasters/answer/2648487?hl=en

As Michael said, getting Google to actually recrawl/recache all of those pages can take quite a while. With the ad gone, it's probably a non-issue and they'll eventually clear out, but disavow would remove any lingering doubt.

Unfortunately, there's no way to tell if you've been penalized without knowing more about the site, traffic, etc. I'd say its unlikely for a paid link from a single site, especially if that link was subsequently removed. Googles isn't usually that aggressive about it, especially if your site generally has solid authority/reputation.