How to delete duplicate files from flash memory?

Hi, can anyone tell me how to delete duplicate files from my flash memory? Every time I delete something in my flash memory, it reduces the free space instead of increasing it. I tried clone-spy, and it showed hundreds of duplicates on it, I have deleted a few hundreds but not all. It says that I have deleted more than 5000Mb, but when I check it up on my flash memory it says it only deleted ca. 80Mb. What did I do wrong?
Any advice very appreciated.