The input frequency (Fref) to the PLL Phase Frequency Detector (PFD) is FREF = FIN / N.
Depending on the fitter selected phase-locked loop (PLL) parameters, the settings might not be optimized and causing the reported FREF to PLL PFD to be over the maximum frequency value reported in the device data sheet.
This affects PLLs in integer mode.
This occurs in the Quartus® II software version 12.0 and earlier.
If your calculated FREF is over the maximum frequency specified in the device datasheet, you can use fractional PLL mode until this is fixed in a future version of the Quartus II software.
This problem will be fix in future version of the Quartus II software.