What type of USB drive are you using? I use an external 500gb USB hard-drive and cannot replicate your issue, but mine is (pretty much) permanently connected.
I always manage items I am copying over in folders, so when I add new files they get copied to the external drive in a folder. If I do inadvertently duplicate something the only place it is likely to be is in the previously copied folder, and it is a simple matter to check.
One other point, when you have copied items to the external drive are you still retaining the files on the main drive or are you deleting them? - Thanks - R.