I find two queen hives at about a 10% rate. It's more common than you think. And probably is a reason for failure in introducing queens for some beekeepers.
Usually they will choose one and cast the extra off in a fall swarm, although some do go through winter with two queens. Most two queen colonies are mother/daughter. Two daughter queen colonies are rare.
It's one of the pitfalls in using strong full size hives for queen rearing. You find the first queen and remove, then put a graft in. And nothing works out because of the second queen. It's happened to me a number of times.