You may see this message in Intel® Quartus® Prime software versions 18.1 or earlier if the Intel FPGA IOPLL IP is encrypted in your design. Due to encryption, the IOPLL's auto-generated SDC file is unable to traverse the atom netlist to find the source of the IOPLL's refclk.
Device Family: Intel® Arria® 10, Intel® Cyclone® 10, Intel® Stratix® 10
Intel Software: Quartus Prime Pro
Last Modified: November 20, 2018
Version Found: v18.1
Bug ID: FB: 1408426345;
IP: Altera IOPLL