Yes, there is a known issue with generating a PowerPlay Early Power Estimator .csv file in the Quartus® II software version 13.0sp1 and earlier for Cyclone® V SoC devices.
When the .csv file is imported into the EPE tool, the I/O power for the Hard Processor System (HPS) functions is counted in both the HPS section and the FPGA I/O section of the EPE tool, resulting in higher estimated power than expected. The HPS I/O power should only be accounted for in the HPS section of the EPE tool.
This is scheduled to be fixed in a future version of the Quartus II software.