Yes, pinout files generated by the Quartus® II software versions 8.0 and earlier report incorrect voltage connections for MAX® II devices using a 2.5-V source for VCCINT.
The operating voltage setting of either 3.3 V or 2.5 V specified via the Operating Setting and Conditions menu is reflected in the PowerPlay Power Analyzer estimates for the design. However, the pinout files show all VCCINT connections as powered by 3.3 V.
Note that this is only a reporting error, you can connect the VCCINT pins on the MAX II device to either 2.5 V or 3.3 V.
This problem is scheduled to be fixed in a future version of the Quartus II software.