SEOs and Webmasters should all be huge fans of Google Webmaster Tools, it provides data and insight into our web sites that we did not always have. SEOs and Webmasters that are educated know what to make from these reports and use the data in an educated manner. There was a good quote at SMX West last week, it went something like, "data is not the same thing as wisdom."
Google Webmaster Tools has often had major issues with bugs, especially in the reporting side of things. The latest bug has to do with the external link reports. Google confirmed the issue saying:
The data shown in your link reports in Webmaster Tools may not currently show links or allow you to download these links for all sites. We are aware of this issue and are looking into it; you do not need to take any action. This will have no effect on your site's performance in search results.
Personally, I am able to see my external links but downloading the report is just lagging for me. I suspect this will be fixed eventually, but just be aware that these types of issues are common in this tool.