Due to a problem in the Quartus® II software version 13.1, 14.0, and 14.1, the Total PLLs in Summary of the Fitter report shows incorrect number when you use Arria® V, Cyclone® V or Stratix® V device.
The Total PLLs should show the total number of Fractional PLLs, CHANNEL PLLs and HSSI ATX PLLs, but it shows only the number of the Fractional PLLs.
To check correct number of the Total PLLs, see Fractional PLL, CHANNEL PLL and HSSI ATX PLL in Resource Usage Summary under Resource Section of Fitter report.
This problem has been fixed beginning with the Quartus II software version 15.0.