YOU HAVE TO REQUEST FOR A REFUND
http://www.cic.gc.ca/english/information/applications/guides/5553ETOC.asp#5553E6
Refunds
To obtain a refund, you need to send a written request to withdraw your application to the Case Processing Centre.
The processing fee is only refundable if we receive your request before processing has begun. Once we have started to process your application, there will be no refunds regardless of the final decision. We will issue the refund to the person indicated on the “Payer Information” section of the receipt. If there is no name indicated on the receipt, we will send the refund to you.
Payment issue – Overpayment
We will:
start processing your application, and
send you a refund.
Note: You do not have to ask for a refund, it will be done automatically.