She cries because he tells her not to talk to him again (rough TL) after she rejects him, realizing that he's always been friendly with her while she's always been shitty with him..
Joonwoo uses this rejection to move on completely from her. Don't think he told her about randchat... she'll regret rejecting him later on when she finds out it was Joonwoo all along, but by that time he will have moved on from her completely imo. Joonwoo hoped she would like HIM, not his randchat impersonation.
Anyways I won't spoil anymore haha, new arc coming up after the latest leaked chapter.