You may see the following errors on physical Channel 4 of PCIe® x8 Hard IP implementation during TimeQuest analysis.
<PCIe instance path>|g_xcvr.sv_xcvr_pipe_native|inst_sv_xcvr_native|inst_sv_pcs|ch[4].inst_sv_pcs_ch|inst_stratixv_hssi_8g_rx_pcs|wys|clocktopld
<PCIe instance path>|g_xcvr.sv_xcvr_pipe_native|inst_sv_xcvr_native|inst_sv_pcs|ch[4].inst_sv_pcs_ch|inst_stratixv_hssi_8g_rx_pcs|wys|observablebyteserdesclock
Physical channel Ch[4] in PCIe x8 hard IP implementation is used internally, but not as a data channel. Hence, these illegal clock warnings associated with Ch[4] should not affect the link operation.
You can safely ignore these warnings.
This issue is not scheduled to be fixed.