I think Crona's eyes change color when the madness inside her/him is taking over. It's not unusual for someone's eye color to change, especially in anime. I don't think it matters much anyway, Crona is always adorable.
Chrona's eyes change colour due to the madness (I assume from years of loneliness and rejection) inside of him/her. When Chrona's content, happy, или any good emotion, Chrona's eyes are a dark indigo-navy colour. When overtaken by his/her madness или when Chrona's upset, angry, frightened, nervous (always o3o), или surprised/shocked, they're lavender with navy-violet edges.
Hope it helped!
(And if someone responds saying 'omg Crona's a gurl/boi', I will disown you. >.> )