bountyhuntergirl86,
Did any Steam Locomotives ever run on the tracks? If so, it might just be a by-product of coal being burned in the firebox below the boiler. However, they could be some type of raw ore brought in with the other Railroad gravels! See if you can clean some of them up with fine steel wool and soapy water, dry then post a few more pics on here. Maybe then, we can Determine what they area!
Frank