Enable the Filter Robots feature under Dashboard > Pretty Links > Options > Reporting. Robots constantly crawl websites; enabling this option prevents known robots from being counted in your clicks. It works best when the Extended Tracking Tracking Style is also enabled.
It’s also a good idea to add your own IP address (whatsmyip.org) and your website’s IP address (whatsmydns.net) to the Excluded IP Addresses setting in the Options. This prevents clicks from those sources from being tracked, which further prevents skewed click reporting.
Because each tracking solution uses different filtering methods, the numbers are unlikely to ever match perfectly, but the steps above help bring them closer together.