WMT measures clicks from Google. This data is gathered directly from Google's properties before the visitor sees your website. On the other hand, GA measures traffic based on a script on your website that has to fire and send data back to Google. If this script doesn't fire, no data goes to Google.
There are multiple reasons why this script may not fire, including mistakes during implementation, someone leaving the page before the script loads, browsers that don't load javascript, security programs that block the code from firing, and so on. All of those factors can attribute to variations in data.
I think it's good to use both sources. When you're in a data-driven industry, it's good to collect lots of it
Here is a post that goes a little deeper, the comments are especially intriguing: http://www.notprovided.eu/why-not-use-googles-wmt-data/