I think I found tour support request at the MU forums. I just wanted to update the forum over here, too.
The suggested solution to return 400 errors and not 500 for non-existing directories is to search for:
RewriteRule . – [L]
in your .htaccess file and to comment it out:
#RewriteRule . – [L]
This solved the problem for me. But the question is, if this is breaking something else? It seems to work for me so far….