Inbox showing unread email but there is none

Go to settings/mail/the offending mail account/and change your "mail days to sync" to No Limit. Then go into your email box to let it start downloading all emails until it finds the mail item that it thinks is unread. This download process will update your phone so that it realizes that the email it thought was unread is actually read. Then go back and change your mail days to sync back to its original setting. The reason it wouldn't update this on its own is because the mail item is older than the "mail days to sync" so your phone is not updating the status of those mail items.