No - CIC is fully aware of the existence of NOC 2006 and NOC 2011 codes, both are valid, but you should use NOC 2011 on your application. It won't matter that the NOC 2006 code is on your work permit, the VO will completely understand that.
Refusals for incorrect NOC codes are for codes that don't match the job duties, or other inconsistencies with the application, indicating that the applicant may be trying to "upskill" his or her NOC from an ineligible C/D level...