You might get this critical warning message in the Quartus® II software versions 10.0, 10.0sp1, 10.1, 10.1sp1, and 11.0 even when you feed a dedicated input clock pin to a PLL in Arria II GX devices.
Refer to tables 5-6 or 5-7 in Clock Networks and PLLs in Arria II Devices (PDF) for accurate dedicated input clock pin to PLL mapping. The input path to the PLL will be fully compensated if the correct clock source is selected according to these tables.
This critical warning message has been removed in the Quartus II software version 11.0sp1.