No, he doesn't know. A lot of their miscommunication happened because they misinterpreted things. You have to remember this story was being told from mc pov. Of course we're able to tell he cross the line. But ml doesn't know anything until mc starts talking about it. He's acting like this because he's upset that things doesn't go the way that he intends it to be - in which taking care of him in whatever ways he could. This is the line that he's crossing. He literally said this before mc cuts him off. Now mc has reminded him clearly about the nature of their relationship, he was trying to keep himself in check.
You will learn in later chapters that in fact, he will not be able to do so.
So basically my guess is the seme realized he's developing feelings that's why he's trying to asshole his way into denial