After 2-3 weeks I notice small white "knobs" in clusters on cuttings that I've placed in water to root. I'm able to scrape them off with my fingernail. Are these scales? Is there a way to prevent them...and... what's the best way to eliminate the algae that grows in the vase during this process?
Without seeing the "knobs" I can't be certain, but what you're describing sounds like root initials. Don't scrape them off! These are the beginning stages of root development. They will eventually elongate and become full-fledged roots.
One way to prevent algae formation in the water is to exclude light from the vase. You can use a dark colored vase or wrap it with something such as foil.