Per the 802.3 1000BASE-X receive state machines, GMII_RX_ER should be asserted, but the MAC layer still marks the frame as bad because there is a Frame Check Sequence (FCS) error.
This is scheduled to be resolved in the next version of the core. In the meantime, a patch is available for v11.1 of the core. Please check
(Xilinx Answer 40625) to download the patch.