Yes, there are known issues with transceiver HSSI pins definition in Arria® II GX IEEE 1149.6 BSDL files.
All the HSSI pins (p/n pair) will need be added to the GROUP_GROUPING attribute.
Also the p pin of a HSSI pin pair will need be added to the AIO_Pin_Behavior attribute.
The pre and post BSDL automatic file generation will be fixed in a future version of the Quartus® II software.
This is fixed in and is available at Arria II GX BSDL Files.