Some copy protections like safedisc 2 have large amounts of bad sectors in the first 800-10000 sectors. They should be copied as they are if you want an exact copy. This can take quite a lot of time, however there is a trick to do it in 5 minutes instead of an hour or more. If you want to use this trick, you'll have to install Daemon Tools first. The trick is called "Fast Error Dump" and is really easy to do, read more about it at the end of
Vluka's FAQ. Otherwise, you can leave CloneCD reading, it will take about an hour but it will get through it.