I have seen that problem talked about before but on my break at work so can't link it for you. Maybe trying deleting the account and re add it?
Sometimes this happens to me, I'll bet if you log into your gmail from a pc you'll find those emails there showing up as unread. The way I've come to avoid it is by backing out of my emails when I'm done reading them rather than hitting home, seems to work for me. Sorry if this has nothing to do with your problem just seems like its what's going on.
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So strangely enough my phone started doing the same thing this am. Said I had 1 message even though I had non, and when I logged into my account online all the messages I deleted from phone were still there. So I went it and cleared the cache from the gmail app and it fixed it. So if you can find that program that will fix your problem not sure why its not listed though.