I faced similar situation. While filing GSTR1 for one of my clients, who is a wholeseller of having many HSN codes. The spread sheet that was extracted from the application, where single invoice having multiple items & multiple tax rates; we considered the same invoice number and invoice value as it is for all three line items. For Ex: Invoice # 001 having total Invoice value of Rs.10,000 with three different rate of items, i.e. 12% for Rs.2,000,18% for Rs.4,000 and 28% for Rs.4,000. We mentioned invoice # 001 and Invoice value Rs.10,000 for all three items with their respective taxable value in B2B section. While uploading the GSTR1 in to the GST portal, the system only considered one line item and removed two others as duplicate invoice details. That means the application is developed in such a way that only takes into consideration the invoice number as reference and excludes other details of the row. In consequence, there is a mismatch of total taxable value and tax on it. Really needs to be fixed.