Linux – Why does wget from ftp-sites sometimes create a few empty files when it downloads the rest of the files without problems

The exclude directories option is:

--exclude-directories=List

not --exclude-directory as you have included in your question

from the wget man page

-X list
--exclude-directories=list
   Specify a comma-separated list of directories you wish to exclude
   from download (@pxref{Directory-Based Limits} for more details.)
   Elements of list may contain wildcards.

Depending on the tool you use it's possible to automatically hash and verify the downloaded files, the only tool that can do this that comes to mind immediately though is the DownThemAll! addon for Firefox.

What I normally use for situations like this a hash manifest file created by md5deep on Windows, you can use md5sum if you use Linux/UNIX or md5 on OS X. Using md5deep I CD to the folder containing the files to be transferred and run the command:

md5deep -l -r *>manifest.md5

On the remote end after transferring the files and manifest you would run the command:

md5deep -l -r -x manifest.md5 *

And it will show a list of every file that DOES NOT match the hash value in the manifest.