Alternator question

I hooked a wire to what he said was the ground and with the ignition on I touched it to the alt case and got a spark...this can't be right?
Looks like someone has tied the brown wire from the ignition into the MSD box as well as the blue wire to the voltage reg. I am thinking cut the brown wire to the reg. The brown from the ignition could be supplying power to the reg constanlty
AL