Card getting charged twice after Apple ID has been created.will it get refunded

Yes, your card issuer should remove it (it may take a few days). Each time that you add or change your card details on your account a small temporary store holding charge may be applied to check that the card details are correct and valid and that it's registered to exactly the same name and address as on your iTunes account.

Store holding charge : http://support.apple.com/kb/HT3702