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Having been taught to believe that true faith can move mountains, it never occurs to the boy that God will not grant his petition.

Could you help me parse the above sentence?

Can I say that "Having been taught to believe..." is a participial phrase, and it wrongly refers to "it", which is the subject of the sentence?

It actually refers to "the boy".

Having been taught to believe that true faith can move mountains, the boy never imagined that God would not grant his petition.