DTJ, usually you have a schematic from which you'll import your BOM references, each one having a unique number. So, even if you can add BOM refs manually on BOMER, ideally you'll always import it from a CAD software (EagleCAD, Kicad, etc) through a CSV file. Those nuts would probably be associated to holes you put on your design.
When writing "2x M2.5 nuts" you are not telling where they'll be used.