The issue occurs because of corrupted data in the fields AMTTAXLIN1 and DEDTAXLIN1 in PINVOICED on the line 1 of the purchase invoice. The VAT value of the second line of the same product is added to these fields on line 1.
The issue has been resolved in Sage X3 2026 R1 (12.0.39) under the reference X3-363239.
Due to the severity of the issue a hotfix is also available for Sage X3 2025 R2 (12.0.38).
Please note the fix does not enable existing invoices with the error to post. These will need to be manually amended.
Purchasing - Purchase Invoices - Create a new invoice for any site and supplier. In the lines section set the Source to Miscellaneous and enter any product at any value above zero. Ensure the tax rate used is not zero.
Create a second invoice line identical to the first.
Complete the rest of the invoice details, save and click on Post.