I had this problem, once immediately after I got a man of the hour promotion- my 300 strong English defeated a 1500 strong Milanese force and the captain got adopted. I ended the turn, and one of the skulking inquisitors turned up and presumably attributing my man's victory to witchcraft, executed him.
To be fair, I had been excommunicated.
To counter this bothersome activity, I've built abbeys and things everywhere, infested my lands with priests and so far have had no more trouble with the inquisition.