A successful cloning of a hard disk is you get exactly a mirror image of the original.

The bad sectors in the original can be physically corrupted areas. They cannot be read and so cannot be written on the new disk. Thus the physical damage is not transferred. All you have is the partition has a few minor holes in some of the files.

The easiest is to delete the damaged files. No need to reformat the disk unless the OS depends on the damaged files. In such a case your system should not boot.