It's not Samba, it's the OS X client. Since the Samba share doesn't support Mac-style file attributes (resource fork, type&creator codes, Finder flags, extended attributes, etc), the OS X file system will split the file into the AppleDouble format, storing the data fork (regular file contents) as one file, and all of the unsupported metadata in a second file with a "._" prefix on the name.
I don't think there's any way to stop the OS X client from doing this (there's a way to prevent ".DS_Store" files, but that doesn't work for the AppleDouble files). There are various programs and scripts that'll remove the AppleDouble files (e.g. BlueHarvest). Unfortunately, for some file types they're actually an integral part of the file (these are, of course, Mac-specific formats like Finder aliases), so depending on what kind of files you're storing, you might wind up deleting something important.