Unconstrained clocks may be reported in the Timing Analyzer Clocks report when the PLL reference clock is shared across multiple Intel® Stratix® 10 EMIF IPs because the PLL reference clock wire is routed to unused PLLs in the I/O column and the Fitter recognizes those as clock resources.
For example, you may see a similar unconstrained clock message as shown below.
emif_ddr4_1|emif_ddr4_1|arch|arch_inst|pll_inst|pll_inst~refclk_Duplicate_4~io48tilelvds_0/s43_0_0__ioclknet48_tile__ref_clk0.reg ; ; Base ; Unconstrained ;
You can safely ignore these unconstrained clocks because they are not used in the design.