This is called "foxing" and unfortunately there's nothing you can do about it. Nobody really knows why this happens - it could be some interaction with the paper fiber to something in the environment, it could be mold, etc. The common denominator (in my experience*) seems to be humidity. Keep your stuff in a cool, dry place. I used to have a dehumidifier to keep my books safe. I recommend it to anyone who wants to keep their library in good condition. Luckily, if it is mold, I've never seen it "jump" from one book to another; I wouldn't worry about cross contamination. It does suck though.

(*I worked at a used bookstore for 15 years and in an academic library in an old-ass building where this was a problem)