Vat returns late filing fees

dear sir

i migrated my company from vat to gst and already closed my company and surrendered my gst number online and its cancelled successfully. recently i was just checking if all is in order and i came to know that my CA had filed the vat return for april to june 2017 that is the 1st quarter late and due to that i am seeing in the website of mahagst.gov.in under section of return dues 1000 rupees as late fees twice that is under CST and VAT

i already had applied few months back to cancel my vat number online becoz i heard that it should also be cancelled even if we are migrated to gst. i got the cancellation order by mail for both the number ending with C and V from MGSTD

now my CA says no need to pay that 1000 rupees but my question is should i pay that or leave it

if i leave it then will it create any issue in future or is it better to pay and get rid

its not yet showing any interest or other charges but its showing only 1000 rupees to be paid as late fees

please advise

thanking in advance