Income tax-itr-4 defective returns u/s.139(9)

Dear Experts, I have e-filed the return of income of my clients by offering more than 8% of the profits. But due to offering other income it falls under the category of ITR-4 instead of ITR-4S. Further i am using IT software to prepare these returns. While offering all the details it automatically computes and prepares the return. So the Income offered u/s.44AD is directly shown under the Business or Profession under particular section in ITR without showing any Turnover/Gross receipts details.Now my clients getting defective notices for the same in various dates. Even though I have also responded through online for the defective returns still i got the notices. Some of the returns were belated returns. Insist me that any other option to file rectification or revised return for the defective ones? If not, what is the remedy for the same?