I found these black dots on both the apples and leaves. They are dome shaped and they come off intact using my nail. Sometimes without leaving a mark on the apple and sometimes leaving a mark outlining where they were but not seeming to penetrate the skin.
They do look like scale. Never seen them on leaves- they are usually clustered on fine wood. If you look under magnification you should see little yellow circular things moving around on your stems if they are an issue on the tree. Scale can actually kill trees but obviously weaken them long before that should happen.