I think it's more common than people think, because you stop looking for queens when you find the first one. I've never had 3 queens that I know of. I've had double queens 3 times that I know of and I've only got a dozen hives. My case, like yours, found and pulled the marked queen, the went on to rob a couple of frames and found a second. Then last month I pulled my favorite queen to get queen cells, put her in a nuc, went back ten days later to collect the cells.... No cells! Sure enough, after a frame by frame inspection, found a second, laying queen.
Cool stuff! Of course you have to wonder how great the queen is now. Like me, my favorite queen, was really 2 queens!