Honestly

It’s not a typical “misunderstanding” or “miscommunication” trope. It’s not like Nathan would believe his story right now, and when they first reunited and he attempted to apologize and potentially tell him what happened, he got a “save it, I don’t care. Don’t talk to me.” Alex isn’t the kind of person to persist after that, so there is no way he would have. It would have sounded like an excuse. I don’t blame Alex for how he is reacting to this, he is caught up in a constant state of self-hate and self-blame, he thinks every bad thing that happens to him is something he deserves.

And Nathan wouldn’t have even believed him. And the only reason he knows about it and believes it in later chapters because he hears about it from other people first, I believe.

And sure, he could have told Nathan when they were younger but he did what he thought was best because he felt like he was in trouble that he couldn’t get out of and didn’t want to drag Nathan with him. He did the best he could have for how he is characterized.