From a Mac you just pass documents to the ereader by drag and drop, and that clutters the file system with ghost "._*" files, Spotlight stuff, FSEvents stuff, etc. You don't see them because the interface hides dot files, but wanted to have a clean SD card anyway.
In addition, Mac archivers like zip(1) or tar(1) and utilities like cp(1) and friends put resource forks and other stuff in hidden files as well. So, for instance, if you untar one of those on Windows/Linux/whatever you'll get that HFS baggage. Ever saw a directory "__MACOSX" out of nowhere? I learnt this the hard-way.
Solution: I wrote unmac, a portable command-line cleaner of those Mac-related spurious files.