Are you sure? Wouldn't that mean that the religious head of the shia religion was sunni? Can the game handle the leader of a religion not being of that religion?
It can happen organically. This was many many patches ago, but when the Mongol Empire would reform the Tengri faith after conquering Constantinople, the religious head title would get conferred to the Ecumenical Patriarch. Back then, the reformation mechanic would grant the pagan religious head title to the highest-ranking theocratic vassal, even if that vassal was supposed to be the head of another religion! I'd imagine that certain mechanics would be broken, but the title could be simultaneously held. In that game, I think that the Patriarch-High Priest wasn't able to call Great Holy Wars for Tengriism because the Orthodox religious head title couldn't call the equivalent war.
I haven't checked it myself for the OP's situation, but my gut makes me think that calling a Jihad for the Sunni faith would prevent him for doing so for the Shiite faith and vice versa.