Are they really small and initially look a little red? If so all you are doing is breaking some of the blood vessels when you are scratching. It's called petichae. This can happen all over your body. It's not dangerous. There's a chance you can get a little scarring if you do it too often.
Do you know why your breasts are itchy? Is it your bra? Are your breasts still growing - this can make the skin itch?
One thing you may help is to moisturise them ie sorbolene or even some other body lotion and it may help not to use soap on them - used a body wash instead as this isn't as drying on your skin.
Also sweat can make them itch so hygiene is important.
i think i have something similar to that. im 14 too, and i think i have big nipples? :L:L but i dunno, and my breasts are slighlty large and also itchy. but i dont have the spot things on my actual breasts, on the bit where your breast joins the rest of your body at the bottom i have a few there and i have some on the actual nipple. i think youre fine :P