I have a full drawer of different disks, any storage size and any physical size, rotating or solid, you name it.
I am experiencing this problem no matter what copies what onto what else.
And I have failed at isolating one reason for it.
I noticed it first in Mountain Lion, when trying to dupe an SD card from the MBPr15 built-in card reader onto a different one stuck in a USB adapter. Which I blamed at first, just to find out that it had no part in the failure.
I tried to copy the same SD card onto the internal HD, and when it failed, now I blamed the SD card, of course. After reformatting it, I re-installed OS X onto it, and tried once more. Just to see it fail again.
Fast forward one year and a half later: brand new MBPr, right out of the box. As in now.
Need to copy a ~500GB library onto it. It failes like the one machine before, saying "The operation can’t be completed because an item with the name “.DS_Store” already exists.".
I truly don't know why, and I can't say I have a solution.
But I started to use a specific method, though, that got rid of the problem.
Once for all, pronto, finito. It never fails, it does not dodge files, it does not delete them.
Maybe someone might find it useful, too?
I'm not proficient at command-line, don't remember enough basic commands to perform all file duties in there, but I know from experience that when something fails to deliver in the "windowed" world, you switch to the parallel, command-line universe, and it always works (because of .bash_history, yep), but it does.
Anyway, I have installed an OS X port of a file manager named Midnight Commander, or simply mc, that exists under Unix, DOS, Linux since the dawn of creation; mind me here, there might exist a thousand other file managers that do the trick, but I stuck with the only one I know, and it's been this one since I was young.
First: look up Midnight Commander for OS X, locate a repository from which you feel comfortable to download.
There's a developer that's made a .pkg installer that never let me down.
Now, from within a Terminal session I launch Midnight Commander as a super-user:
sudo mc
After entering my password (as an Administrator of my own machine), I now select whatever I need to copy, point to where I wanna copy it, hit F5, end of story, Roger and out.
It's not THE solution to a bug, or whatchawannacallit.
It just works, it's free, and it promotes a bit more awareness of the Terminal even to non-geeks users like me.
And, it comes in handy whenever I need to move these 400GB of audio files, which is once every so long or half.