Applications folder/Utilities/Disk Utility will allow you to repair permissions and verify your hard drive. To repair some permissions and to attempt to repair the hard drive, you will need to boot into the Recovery Volume (command - R on a restart or hold down the option/alt key during restart and select it) and run Disk Utility there.
The OS will automatically assign bad sectors as unusable (in fact I think HD firmware manage it).
Disk Utility in recovery mode will do a better job than chkdsk on a PC which won't understand HFS or the automatic 'adaptive hotfile clustering' that in effect defrags & stores the most important files in the fasted disk regions. Files over 20mb are also defragged by the OS automatically.
This old document covers the basic concepts
There are 3rd party tools to defrag Mac disks, but Disk Utility is safer. Run the verify/ repair tasks on the boot disk & also run the repair permissions task too. Picking the wrong tool will make performance worse.
If the error persists post more info, like where the file was, what app was copying etc.
Ok, I have run disk utilitiy from a recovery partition but no complete luck. When I am still transferring files i get (error code -50).
Let me start by saying I started with this drive formatted as ExFAT so that my files could be viewed by both Operating Systems. Then converted it to HFS after I read, and experienced many problems with Mac OSX corrupting the drive somehow. But now I am still getting (error code -50) when copying files to an external HD on my music files.
So I am thinking that there are some type of permission error on those specific files, or sectors that somehow corrupted from the ExFAT partition?
To copy any large batch of files I usually have more success when I transfer it to my main SSD boot drive, then to where ever else
*This especially happens when transferring files to my Windows 8.1 computer shared drive on my network*