Sir,
According to Section 16 (4) of CGST Act, 2017 "a registered person shall not be entitled to take input tax credit in respect of any invoice or debit note for supply of goods or services or both after the due date of furnishing of the return under section 39 for the month of September following the end of financial year to which such invoice or invoice relating to such debit note pertains or furnishing of the relevant annual return, whichever is earlier :
In your case you have taken the ITC in GSTR-3B return pertaining to May 2018 which shows that you have taken ITC before 20.10.2018, that is, due date for furnishing GSTR-3B return for September 2018 following the financial year 2017-18. Therefore you have taken the credit correctly. Therefore no amendment of GSTR-9 return is required.