There are notes in the Stats pages about how WordPress.com stats tracks visitors. "Hits" is an archaic method as many WordPress Themes feature the ability to allow page loading, switching, and comments to change on the web page without triggering a "hit."
WordPress.com stats do not count your visits when you are logged in. There are many other differences. WordPress.com Stats developers have worked for many years to keep the stats as accurate as possible but no stats counter program is completely accurate. All track stats a little differently so it is like comparing apples to oranges.
I've found ways of comparing multiple stats and analytics data to find an average among them to give myself a better idea of what's going on. Or I just use one and trust it. Up to you.