Due to a problem in the Quartus® II software version 12.1 SP1 and earlier, you may see one of these internal errors during compilation if you are using Partial Reconfiguration. This error can occur if you have a Dual-Regional clock that only has fanout in one quadrant.
To work around this problem, either change these resource to Regional clocks which only cover one quadrant or ensure that the clock has fanouts in both quadrants.
This problem is scheduled to be fixed in a future release of the Quartus II software.