GSTR-4 late fees...

The information you might be working with may not be fully updated. While there have been instances of extended deadlines for GSTR-4 filing in the past, the current due date for FY 2024-25 remains April 30th, 2025 as per latest notifications. The system might be calculating late fees based on this default date. It's possible there hasn't been an update reflecting the potential June 30th deadline extension discussed in the recent council meeting.

If the extension is confirmed, there should be an official notification issued by the GST Council. You can check reliable sources like the GST portal or official government websites for updates on the GSTR-4 deadline to ensure you're working with the most recent information.