Why would a domain show up in Webmaster Tools but not latest links?

[EcommerceSite]

I am going through links and trying to figure out what to disavow. I found a domain under "Who links the Most" I wanted to see what the exact link was and I can't find it when I download all links. Why would that be?

[gazzerman1]

The only thing I can think of is that Google's John Mueller has said in the past that they only show a sample of links not all the links which has been a giant pain for many trying to do clean ups, however they have also said if it is not in WMT latests links then you need not bother with it as part of your disavow.

However if you are aware of a link and you think it is a poor one that you want to disassociate yourself with then I would add it and make a note about it if you are also in a penalty that needs a reconsideration request. It shows you are looking further than the bare minimum.

[EcommerceSite]

We aren't in any sort of penalty, the site has been around close to 14 years and over time it has just picked up some crappy links. I figured it would be a good idea just to be proactive and get rid of stuff that I know is bad.

[Chris661]

I have seen links reported in GWT that when I clicked on were not there. I like to look at the page source and search for the link just to see if it might be hidden. But all I can guess is the GWT data is old and the link is no longer valid. Recently I read this article by Marie Haynes http://searchenginewatch.com/article/2374406/Penguin-Recovery-Should-You-Be-Removing-Links-or-Just-Disavowing   and asked her in the comments what she thought about proactive disavow. Take a look but basically she says if you have no history of shady spammy links, you have nothing to worry about. But please read her words as she is very respected in this area.

[EcommerceSite]

We have never done anything blackhat or spammy, but over time we have just acquired crappy links. We had a traffic drop when the first penguin was rolled out so we thought cleaning up some of the old crap would be a good idea.