I’ve had this problem as well.
Here’s another thing that can cause dupe files: Different bit rate…I think that could create dupe files in anything.
This should not cause duplicate files/folders to be created. At least it never has on mine. I have some FLAC, mp3 (at various bit-rates) and even a couple WAV files on mine. There are no duplicates.
Unless of course you have 2 or more of the same file ripped at different bit-rates. As you can’t have more than one of the same file name in the same folder, it’s possible it might create another folder to house the 2nd one. But in my experience, whenever I try to transfer a file where one already exists in the target location, whether it be an audio file or any other type of file (Word .doc, Excel .xls, .pdf, etc.), I’ll get a message stating this file already exists, and asks do I want to overwrite the existing one? It also tells me the date and size of both the files so I can determine if indeed it is a duplicate or an updated one where I do want to overwrite the old version.