It’s actually a good perspective to compare Mashiro and Misaki in the emotional department. Mashiro has trouble identifying her feelings while Misaki has trouble understanding why Jin rejects her. It’s as if Mashiro and Sorata’s current relationship was how Jin and Misaki were, back when Misaki just realized her emotions for her childhood friend.
But perhaps, Misaki too realizes her fault. Maybe, deep inside, she wants Jin to punish her. To mess her up, and leave her. I guess what’s eating her up is the guilt. The one where she realized how her genius, her very existence, was able to put pressure on her dearest friend. That Jin had to put up with her very being despite being crushed by it.
And perhaps, she is unaware of what Jin truly desires. Maybe she is so engrossed in receiving her punishment that she fails to acknowledge what Jin’s message, his rejection means. Will they be able to make-up before Jin leaves or will it be a sad farewell?