Description
You will get this error message in the Quartus® II software versions 12.1 sp1 and earlier when you place a 2.5V input pin in a I/O bank powered by 3.3V in Cyclone® V devices.
This is a software issue and not a device limitation.
Resolution
You can assign the 2.5V input pin to be a 3.3V I/O standard to avoid the error until the software is fixed.
This is scheduled to be fixed in a future version of the Quartus II software.