Ok so i have this theory. You know when Dean and Cas look at each other for a long time and Cas makes the little cute confused face. I can’t find a good gif but he does the little head tilt and squinty eyes thing. Anyway, in one episode with Claire, Cas tells Claire that he can not only sense prayers, but can sense a longing too. My theory is that when Cas and Dean are making intense eye contact, Cas can sense the longing and even lust that Dean feels towards him. That’s why he looks confused, because he’s trying to work out why Dean is longing for him.