I am very concerned by many of the posts here. I think the message this young man is giving is not being heard.
If a young man, from a home where jeans are not worn, perhaps not acceptable, and goes to a yeshiva where jeans are not worn and perhaps not acceptable, then the wearing of jeans is sending you a message. He WANTS you to ask why !! He is making a statement with his clothes that, perhaps, he is afraid, or unable to do with his mouth.
Any “unusual” dress is a cry for a conversation. Not an accusatory tone, simply a query as to why. Watch his face and body language more than listening to his words. If you feel uneasy, you need to speak to a Rav who knows and understands both your son and your family for guidance.