proper sealing & installation of crab orchard

Hi! I recently had crab orchard steps and a front stoop installed. Within a week, the steps developed black dots and the stoop developed large black areas. it appeared to be mold. an interesting side note is that a piece of crab orchard stored in the garage also developed mold. (so that seems to rule out faulty installation as the cause.) the contractor has cleaned the areas with an acid wash. it helped significantly but black stains and the black dots remain. could the root cause be shipping the stones without proper cleaning? or perhaps do to improper sealing (does crab orchard need to be sealed?) also, any advice on next steps? thank you for your help. any info would be greatly appreciated.