You get this warning in the Quartus® II software if you implement the assignment specified in the Transceiver Clocking in Stratix® V Devices chapter in volume 2 of the Stratix® V Device Handbook.
The incorrect setting is:
set_instance_assignment -name INPUT_TERMINATION OFF -to <refclk_pin_name>
The new recommendation is:
set_instance_assignment -name XCVR_REFCLK_PIN_TERMINATION DC_COUPLING_EXTERNAL_RESISTOR -to <refclk pin name>
This problem is fixed in the latest Stratix® V Device Handbook.