FileZilla Issue

Hello. I tried using Filezilla to transfer some files and I keep running into problems. I transfered data once, and anytime I try to repeat the process Filezilla says there are already copies of those files in the destination folder. This is impossible as the destination folder is empty. Even if i try changing the folder, it says the files exist and need to be overwritten. If you try overwriting them the thing just crashes. If anyone has any ideas, I am open to hearing them as this is really pissing me off.