If the holes you refer to are the ones that attach to the BB spindle, you can take the spindle out (or leave it in the BB) and paint the square ends of the spindle with Dye-Chem and push the cranks onto the spindle ends, then remove the cranks and inspect the Dye-Chem for uneven rub-off. This will show even minute mating surface irregularities. Generally, however, spindle holes worn enough to cause problems will be apparent just by looking at and feeling the cranks when pressed onto the axle.