Make sure you disable full disk encryption prior to cloning. Also, remove any administrative profiles set up on your system before cloning, or the cloning process fails.
There are normally multiple partitions on the boot drive, the cloning tool moves them one at a time. The size of the partitions also varies, so some complete faster than others. Even if one of the partition cloning operations fail, the others clone and complete. Trying the cloning operation again usually fixes the problem.