This may be an issue due to a mismatch in pin names of the IBIS model and the pin names in the actual design. This warning message is actually covered in TechNote MG59548: Handling Pin Mismatches between the IBIS Model and the Part Used. You will need to ensure that you ref file matches your actual design. Therefore you will need to either edit the IBIS model to match the part on the board or manually assign each pin model to the pin on the board. If you see no inconsisitencies then we may need to open a service request for your issue to be able to determine the actual cause of this issue.