Interesting, I'm not a believer in problems that solve themselves. Before I was thinking, someone had wired something wrong and you would find it and that would be it. The good news is, when these cercuit are joined you didn't get 240volts and burndown the house and the breaker did kicked off. While this is working fine there is still a problem and finding it would be imposible maybe.
I would still map out where these wires go and where all the connection are. You could have something as hard to find as a nail thru a three wire which could change with humidity in the house.
Finding where two wires are in close prox to each other shouldn't be hard.