Yes, there is an issue with the post configuration BSDL file for Cyclone® IV E devices that is generated in the Quartus® II software version 11.0 SP1.
When device migration is enabled in the Quartus II software, the extracted post configuration BSDL file has an error. For pins which function as I/Os in the currently selected device, but function as power pins in the targeted migration device will be printed as usable I/O pins which are not supposed to be in the post configuration BSDL file.
In order to avoid the error in the post configuration BSDL file for Cyclone IV E devices that is generated in the Quartus II software version 11.0 SP1, turn off device migration.
This issue is fixed in the Quartus II software version 12.0.