There are a couple of fungal disorders that can cause this. There is now need to throw the apples out though since it is a cosmetic issue, not something that makes the apples inedible or unusable in any way. If you want perfect apple though, you’ll have to spray them regularly starting in spring with a fruit tree spray that contains a fungicide. If you drop by the garden center in April, we’ll set you up with what you’ll need.
Here’s an article you might find helpful: https://hortnews.extension.iastate.edu/faq/there-are-black-spots-surface-my-apples-can-i-eat-skins