Due to a problem in the Quartus® II software version 12.1 and earlier, you may see warning messages for invalid Fitter assignments when using ALTDDIO_IN or ALTDDIO_BIDIR megafunctions if your design targets a device family without dedicated DDR input registers. In these device families, the DDR input registers are implemented with three internal logic element (LE) registers.
The warning messages can be safely ignored as the DDIO_INPUT_REGISTER assignment is not valid for devices that do not have dedicated DDR input registers. Refer to the respective device handbook for further information.
This problem is scheduled to be fixed in a future release of the Quartus II software.