If you used a DOS copying utility from a DOS prompt within Windows, then
many files will have been is use and would not be copied, or would be copied
in an invalid state, as you have discovered.

A cloning procedure will usually require a boot to DOS, not only to ensure
that Windows will not have the files in use and prevent them from copying,
but also because if you need to use the clone to restore the system then
there's a good chance Windows won't be running and a boot to DOS is probably
the only way you can use the machine.

I don't think it's practical to use something like XXCopy from a DOS prompt
within Windows and then create separate copies of those files that are in
use and don't get copied.  It would be simpler to use a proper cloning
utility from a DOS boot.  I suspect that XXCopy could do that, but there are
commercial cloning utilities available that exactly address these issues.