Well, I've figured out what's causing it. It's happening when users are hitting "post reply" multiple times. The software looks for duplicate posts and won't actually submit the post to the database if it's an exact duplicate but it looks like it still sends out the notification. I'm going to submit a support ticket to vB and see if they can change how it's handled in future versions.
Kudos to Steve for figuring it out. Seems like that's a really obscure thing to be able to find. Maybe vB will issue a "patch" for it, like Mr. Gates does every time the stuff hits the fan with Windows.