When using the EMIF debug toolkit on your UniPHY-based memory controller design in Quartus® II software version 12.0, you may experience the internal error specified above. The problem is due to a conflict between the resources of the serial flash loader and the EMIF debug toolkit.
This issue is fixed beginning with the Quartus II software version 12.1. For earlier releases of the Quartus II software, the workaround is to remove the serial flash loader from the design when using the EMIF debug toolkit.