Why does Sora take that bus from the airport? If she had taken the train and subway, she could have wound up almost next to the Magic Bureau.
For that matter, why doesn't her teacher pick her up at the airport?
Why doesn't Sora go to her teacher's house first the day before, so she can attend classes more leisurely the next day?
Sora is instructed to go to Shimokitazawa station. A simple search on Google Maps shows that she could better go to Ikenoue, from which it is a much shorter walk to her teacher's house. The makers obviously wanted an excuse to let her walk through the bustling Shimokitazawa neighborhood, but she keeps going to Shimokitazawa station from then on as well.
Did she have any opportunity to use Google Maps? If no, then it's unlikely she would find out about Ikenoue being better.
Okay, it's already rather contrived that Sora just happens to be at Akasakamitsuke station during that traffic accident, so she can save the day. But why is there so little interest in her after that? Sure, she gets questioned shortly by the police, but you'd expect the media to be all over this scoop, seeing how she just saved lives in a spectacular way. The police could have given her a lift to the Magic Bureau, at the very least.
Maybe they got used to it with mages being more common there than in real life. And they're Japanese, so some things are different over there.
What's the purpose of Sora's magic spell in the end? Her father said he wanted to see his daughter married, but all Sora did was emulate a wedding ceremony without actually having someone to get married to. She wouldn't even have needed to perform magic; simply dressing up as a bride would have done the trick already.
Even better: she could have married Gouta for real.
Also, why does she have to die at the very moment she casts that last spell? If performing magic would really strain her heart so much, why would she do it? It basically amounts to a senseless act of suicide. It's also strange her mother takes it so well; any real mother would rush her daughter to the hospital, even if chances of survival are slim. Remember: Sora's father had the same condition but grew old enough to marry and have a child. Did Sora have a worse case?
That's most probably because writers wanted to have a bitter-sweet ending instead of a wholly good one.
Why do they have to wrap the dolphins in water bubbles before throwing them toward the open sea? Wouldn't it be easier just to throw them directly? They should be fine as long as they're away from the beach.
Maybe it's easier to keep a living thing encased in water and make water move than it is to throw a living thing? That seems to be a likely case, and it makes sense since a failure to move water with magic means the dolphin falls back onto water, while a failure to move a living being with magic can possibly result in gory death. That, and it's probably also to teach them not to use brute force approach with their magic.