X's displayed on some of the bits in the reconfig_to_xcvr and reconfig_from_xcvr busses between the Reconfiguration Controller and transceiver PHYs in simulation of Stratix® V, Arria® V, and Cyclone® V transceiver devices is expected. These bits are reserved for future use, and can be safely ignored.
If all of either the reconfig_to_xcvr or reconfig_from_xcvr lines display X's this is not normal and connectivity should be checked between the Reconfiguration Controller and the transceiver PHY, as well as clocks and resets to ensure correct operation.