I see, hopefully the clone is successful and everything is fine afterwords, but as I've already mentioned - backing up your data before that is crucial. After you are done with backing up and cloning the drive, once you've determined that the clone works fine, you could low level format the drive with the bad sectors. You can either use an HDD diagnostic tool (most of them have that option), or do that via CMD and DISKPART. After that you should initialize, partition and format as you see fit and re-test it to see what's the situation with the bad sectors.
Here's how to low level format (a.k.a. Write Zeros) it via DISKPART. Open CMD (as adinistrator) and:
1. Type
diskpart and press "enter"
2. Type
list disk and press "enter"
3. Type
select disk X and press "enter", where X is the number of the drive you wish to select. Make sure that you've selected the correct one. You should be able to recognize it by its storage capacity.
4. Type
clean all and press "enter". When the process is finished, you can just close the Windows.
This will write a "zero" and piratically make each individual sector blank, but it could take a lot of time, depending on the drive's size. I know I'm a bit like a broken record, but this is important and I'll say it again - backup, there's no data recover after a low level format.