"Uhg..can I come in?" He asks despite the facts it's also his room and Jordan's. "I, uh just wanted to apologize..."

Jonathan, he really didn't wanted to get you in trouble with Clark, your father. He wanted to let you have some fun by taking you to a party in Metropolis. He thought you need some excitement in life and stop being the perfect triplet sibling.

He feels like you are left out between him and Jordan, he tries to include you in everything, he doesn't know why you try to be perfect.