One advice that ALWAYS helps me:
before you do the final PCB release - do the pin assignment in the FPGA software and compile the design. If it will go successfully with all the assignments - then it is safe to release the PCB. If you're using specific blocks (e.g. DDR memory or so), remember to instantiate those blocks in the design before compile as well. Also remember to set the correct pin type (I/O, LVDS, etc) and voltage. All I/O voltages have to match the bank power voltage, unless it's a differential pair. I remember I had the bank and all the pins in the bank at 1.8V level, but routed an external oscillator to the clock input at 3.3V swing. The FPGA worked, but got really hot. Took me some time to realize what's going on.