The department is legally correct in toto. Not adding additional place of business in the registration application on common portal from where business was carried out is very serious offence. It means unregistered unit. It may have serious repercussions on the client's buyers.
C.B.E. & C. Flyer No. 1, dated 1-1-2018
Amendment of Registration
Except for the changes in some core information in the registration application, a taxable person shall be able to make amendments without requiring any specific approval from the tax authority. In case the change is for legal name of the business, or the State of place of business or additional place of business, the taxable person will apply for amendment within 15 days of the event necessitating the change. The proper officer, then, will approve the amendment within next 15 days. For other changes like name of day to day functionaries, e-mail Ids, Mobile numbers etc. no approval of the proper officer is required, and the amendment can be affected by the taxable person on his own on the common portal. A functionality to update email and mobile number of the authorised signatory is available in the GST system. The taxpayers can get it done by the concerned jurisdictional tax authority. Generally, the amendments take effect from the date of application for amendment. Commissioner, however, has been given powers to permit amendments with retrospective effect.
REMEDY
Now, you can apply for amendment in the Registration Certificate in the Core field on Common Portal System for adding additional place of business. There are case laws in the favour of registered persons/assessees. If no revenue loss has been caused, take shelter of the case laws for not imposition of penalty. You may request for treating it as procedural lapse.