Isak use his mother's problems as an excuse when he don't want to talk about things. Don't know if you remember but in season 1 Eva meet Jonas at Isak's house. And he told Eva that Isak's father had left Isak and his mother. And Isak mother has mentally health issues, (we have not been told any diagnoses), so she didn't take her husband leaving very well. And Isak was really sad, that was why Jonas was there. So when he use that as an excuse he knows that at least Jonas will believe him to some kind of point, and don't bugging him with to many questions. But Jonas also knows Isak very well so as much as he also knows about his mother I think he also senses that something else is bugging Isak.