The command lists (and count) also the directory (.) and the parent directory (…), that’s okay. I think it’s the wrong filesystem for your project. Or you have to create a directory (maybe named “Data”) where you move all your files, because there’s a limit of maximum file- / directorynames in the root of your flash drive with vfat. And with many little files you’ve reached this number. I don’t use flash drives with vfat, so it’s just a thing I remembered from a few years ago.