Become a MacRumors Supporter for $50/year with no ads, ability to filter front page stories, and private forums.
What you described isn’t new. It has been an ongoing problem on Mac and iOS. I have seen a few threads about it. It doesn’t seem to affect everyone and to my knowledge, there is not a “fix” for it.
 
Had the same problem. Drove me nuts. At least for me this worked - in the Mail app I had 'to me' and 'cc me' filters checked. The 'phantom' (but legit) emails turned out to be all from a couple of group email lists that I was part of. After disabling those filters all is well. Also if you're sure there are no real emails awaiting your perusal after selecting the proper mail folder just use 'mark all messages as read' under the mailbox pulldown menu to eliminate the phanton count.

Hope this helps!
 
Register on MacRumors! This sidebar will go away, and you'll see fewer ads.