You killed the army, but you didn't kill all the soldiers.
There are many ways you can destroy an army: killing is only one of them. In these battles, morale matters more than pure killing ability. As you do cut down men and engage aggressively, the opposition will begin to lose heart. They aren't just fleeing the battle, a shamefrul dispray, but they desert. Many flee and avoid their old lives to hide from the shame. Some run from the battlefield and return to their homes, choosing the safety of the plough. Many flee, to be considered as losses for the battle, to reconsolidate elsewhere and rise back up as diminished levies.
So, tons of those defeated soldiers might not actually be dead, the Sultan being one of them. He fled combat, effectively removing his unit from the fight. -1 soldier, as his removal from combat counts him as a loss.