Yes, there is an error with the Arria™ II GX device pinouts in Quartus® II software version 9.0 CB (Customer Beta).
Pin-outs using pins DATA[7:1] and CLKUSR as LVDS differential inputs or outputs are affected. The pairs (DATA7, DATA6), (DATA5, DATA4), and (DATA3, DATA2), and (DATA1, CLKUSR) have their LVDS directions swapped (TX pins incorrectly marked as RX pins, and vice versa). Other pins, and usage of these pins as singled-ended I/Os are not affected.
The work-around is to not use these pins or to wait for the final Quartus II version 9.0 release.