Yhere is nothing in the context and no hint as to why either answer could or could not be correct.
As Maarten and Chris mentioned both are correct.
As per the lesson, 'how come...?' means 'comment ça se fait que...' or 'comment se fait-il que...'
In this kwiz, if it is a multiple choice question, only one of the translations above is given. If it was a written answer, both are accepted.
I hope this is helpful.
I don't know what the choices given were, but both answers you mention are correct.
Both answers correctly written would be right «comment ça se fait qu' » or «comment se fait-il qu' »- you can use either, the latter being more 'formal'. However you have written «comment CE fait-il qu' » above. That would not be marked correct in a quiz.
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