I am currently running a campaign where, in one of the main story arcs, the villain is a rogue(assassin) with the charlatan background. He a very charismatic man who already commands a fair amount of respect and power having lied, cheated, and murdered his way into a position of nobility - his alter ego. In reality he leads an organized crime ring, and has an insatiable thirst for power. Meanwhile the surrounding kingdom has gone to war on a front far from the city in which the villain, and my players, live. The military presence is thin, the guardposts are empty, and the villain is not the sort to look a gift horse in the mouth.
Over the course of the campaign the villain plans to use his crime ring to destabilize the government of the town from which my players conduct their operations. Meanwhile his alter ego will be attempting to win the heart of the people, promising to stabilize the region and keep them safe. In the final stages of his plan he will sell out the criminals he commands, who are oblivious to the connection between his identities, and assume leadership of the region in a populist uprising which the depleted military is unable to prevent. It will be up to my players to keep him from assuming power, or otherwise take him down.
Leading up to the end-game big reveal I want to drop in a few clues that the "noble" is not what he seems. The clues should not be so heavy-handed as to give away the villain's plot on their own, but should hint to my players that something is amiss, and is probably worth investigating. I don't want to let things spiral out of control without giving my players the opportunity to stop it. How can I foreshadow the villain's true identity given this context?