Since the implementation of the new STAR smog check program, smog stations are being very careful in ensuring vehicles are equipped with proper/required catalytic converters. The smog check technician will check your vehicle's catalytic converter EO numbers. If they don't match the required CAT EO numbers for your vehicle will fail the visual portion of the smog check as an "emissions tamper".
Under the new regulation a pre-OBD II (pre-2009) converter can pass the smog check as long as it was installed before 1/1/09 and you can provide the smog station proof of the installation date. If however the installed CAT was not manufactured or approved for installation on your vehicle, it will fail the smog check regardless. The following is a PDF by C.A.R.B. explaining the new California CAT law.
www.smogtips.com/Aftermarket_CAT_ARB.pdf
In this specific case it appears you may either visit the smog check referee's office for inspection, or if possible show the smog technician proof that the CAT was purchased/installed prior to 2009 and ask he/her to retest the vehicle.