It happens to me every few weeks but not enough to concern me.
In case it matters, I use Opera 12.16 with Win 7.
The last time it happened was a day or so ago but I can't recall if it was just before or just after I uninstalled AdBlock Plus when it wouldn't whitelist duckduckgo.com.
I have noticed that every once in a while, a second cookie will show up on the Allow list in CCleaner for a site that's already there.
I assume that now and again a site updates cookies and, because they're not quite the same, they get listed, too, but being no kind of tech expert, that is seriously a guess and may have nothing to do with this at all.
Gil.