Ask HN: Accuracy of Google Webmaster Tools

I began tracking my site's data on Google's Webmaster tools. But a lot of it doesn't make sense, for example I get +2,000 incoming links but when I download a list of "all incoming links" I get an excel sheet of only 250. Also, for how it does with search queries, the number of clicks is almost twice as much as the queries. How is that even possible? Are there any alternatives?