Due to a problem in the Quartus® Prime Software Standard Edition Software version 17.0 Update 2 or earlier, you may see this problem during Fitter stage.
To work around this problem, apply the following fitter setting:
In the Quartus Setting file (.qsf),
set_global_assignment -name FINAL_PLACEMENT_OPTIMIZATION ALWAYS
Or in Quartus Settings,
Assignments -> Settings -> Compiler Settings -> Advanced Settings (Fitter) -> Final Placement Optimizations (Always)