Yes, the CRC_ERROR pin asserts momentarily before INIT_DONE goes high when the CRC WYSIWYG atom is used in Intel® Stratix® devices. This issue does not occur if the CRC WYSIWYG atom is not used.
This will be fixed in a future version of the Intel® Quartus® II Software. In the mean time, if you need to use the error detection CRC feature in Intel Stratix devices with the CRC WYSIWYG atom, you can download the following patch as a workaround for the Intel Quartus II Software v9.0 SP2 using the links below: