It seems that this is an issue caused where the email account uses labels and then Opera's client maps to those labels as well as the inbox. So if you get an email in GMail that you automatically label then Opera sees it as 2 emails - one in the Inbox and another in the mapped label folder. You may also get a third as Opera maps by default to [Google Mail]/All Mail.
So if you unsubscribe to the [Google Mail]/All Mail folder then you should see a reduction in this problem happening. Not sure if it's going to sort it all but seems to have worked for me.