Rejection of service tax return

I had filed Service Tax Return for half year Oct 15 to Mar 16 & Apr 16 to Sept 2016 of my firm with the department before due date without any delay and has also deposited all the service tax with the department within time prescribed. But the return uploaded to the site was rejected by the department on the ground of Incorrect Service Tax Registration Number. but the Service Tax Registration number is correct and legally valid. However, i forgot to check the status of my uploaded Service Tax Return that whether it has been successfully filed with the department or rejected. Now the department has asked to file fresh return along with Interest on late filing. Can someone suggest me that since the reason for which Service Tax Return has been rejected by the department is invalid and the return for next half year oct 16 to Mar 17 has been successfully filed with the department with same registration number. how can i escape my self from the interest on late filing of around Rs. 20000/- each for both half year returns i.e. aggregating to Rs.40000. As there was no discrepancy in the return of any kind in the Service Tax Return on my behalf.