Since all of the Intel® Stratix® 10 SDM IOs support pin muxing, the MSEL[2:1] pins may be seen to drive out high shortly after power up when the configuration mode is selected as Active Serial x 4. The MSEL pins are first sampled after power up and then set as nCSO pins for on-board serial flash device. These pins may be expected to drive out until CONF_DONE is asserted.
This is expected behavior and is scheduled to be included in the next release of the Intel Stratix 10 Configuration User Guide.