Kiritsugu's level of caring about someone sleeping in church hovers somewhere around nil. Sleep is probably one of the better uses of church, in his opinion. Yet it's an infraction, and the boy is likely going to get in some amount of trouble for sleeping during the service. Kiritsugu has no particular fondness for punishment without good reason.

That's why, from his place seated behind Lancer, he cuffs him in the back of the head.