To work around this issue in software version v12.0SP2, modify the auto-generated Qsys top level RTL file to ensure that the following parameters are set:
.bypass_clk_switch_hwtcl ("false"),
.cseb_cpl_status_during_cvp_hwtcl ("completer_abort"),
.core_clk_sel_hwtcl ("core_clk_250"),
.rx_ei_l0s_hwtcl (0),
.enable_l0s_aspm_hwtcl ("false"),
This issue is fixed in version 12.1sp1 of the Quartus II software.