I am pretty certain that what you have going on are the nests of an insect called the gall wasp. In most instances they do not really harm a tree but in certain circumstances and species of gall wasp they can. I know of no means of combating them. You see galls on many types of trees and I would guess you have seen them before on oak trees and it doesn't hurt them any at all. But an apple tree may be different. Check with an arborist.
I should explain more about galls. Most galls are harmless and are caused by insects. In apples there is another gall which isn't a gall but a bacterial infection that looks like a gall. This is called Apple Crown Gall. I cannot tell from a picture which it is. If its crown gall there isn't much you can do and it will probably be fatal to the tree. You need an arborist or extension agent to come look at the tree.
