Why can't some disks be copied?

The reason you cannot copy some of your disks is because the game producers do not want you to - in order to protect their time and investment.

A more technical answer is that the physical properties of magnetic media can be used in many ways to hinder copying of the data stored on it. For magnetic media, it is difficult to read something without knowing how it is structured, and it is impossible to reliably write something without knowing how to write it.

This “how” varies between publishers and game developers, but they used a wide variety of techniques. The whole emphasis in Copy Protection is to write the data is such a way that it can be read, but cannot be written using consumer products, and hence cannot normally be reproduced.