Moreover there is no late fees mentioned in the GST law for ITC-04. Although, the ITC-04 is a tool for informing the commissioner of job work transactions, therefore suggest to file at the earliest.
Yes penalty u/s 125 may be made applicable, although, it could be litigated and waived off for procedural non-compliance.
As per Notification No. 87/2020 - Central Tax, dated 10th November 2020, the due date for furnishing of FORM GST ITC-04 for the period July - September 2020 [ Q2 of FY 21 ] has been extended till 30th November 2020.