Guidance and exmption request of penalty u/s 92(5) for late filing annual returns of previous years due to professional negligence of company ca.

Dear Sir/Madam, I would like to say that, we have a company client, whose Auditor has neither filled Annual returns on time, nor intimate to the company regarding due date of filling of such above returns. Company has not worked during the said periods and turnover is less than 2 Lacs of such periods, i.e. FY 13-14, FY 14-15, FY 15-16. Due to above reasons, company has attracted penalty u/s 92(5). Who is liable to pay above penalty i.e. Company or Company's Auditor (CA). Is there any provisions that can be exempt to the company for pay such penalties? Can company file above annual returns without payment of penalty now and remaining procedure of penalty may discuss later with authorities and departments? What should we do? Kindly guide us and oblige.