He's not eligible for a nonimmigrant visa for the reasons stated, he's clearly in the process of immigrating. As long as he filed for that status change while he was legally present, he is not accumulating illegal presence time while the decision is being made. It's unclear why you filed for a visa he didn't qualify for, but it would seem that this is not going to harm him. If he wants to leave the country, he needs advance parole to get back in at this point. You should consult an immigration attorney before filing any more spurious or worse immigration documents.

