"Do your parents know you're here?" Bruce asks you, serious but not angry. From your expression as you eat the cookies Alfred gave you, he knows that no, you wouldn't come to the Wayne manor from your farm as a surprise by yourself, and Clark hasn't told him anything either, that leads him to deduce that you ran away from home. It's very easy to read your expressions. "I'm not going to call Clark, but only if you tell me the truth about why you're here."