With paper, it all comes down to the fact that it's made from wood, which contains the substance lignin.
When the molecules, responsible for the color (chromophores) in lignin, are exposed to air and sunlight, they become less stable, causing them to absorb more light, gradually darkening the paper from white to yellow.
This is a completely natural process and doesn’t mean that the manga is used or dirty.
Manga with these types of issues won’t be replaced as this is a common characteristic for books in general.