We were so close!
This one is on both of them.
Miyuki has never been clear about her feelings and she is from Kyoto, where people often mean the opposite of what they say.
Sorata has no confidence in himself, so he can't believe Miyuki might actually like him and wants to be with him, not because that's what her grandpa wanted, but because that's what she actually wants.
If Sorata were to ask her if she means the things she says or if she being 100% from Kyoto and meaning the opposite, then he might start to realize she likes him. If she told/showed him she likes him in a way he can't deny, then he would have a bit more confidence and all of this wouldn't happen. If at least one of them tried to actually understand the other person, instead of guessing what the other person wants/feels, then things would be SO much easier for both of them.