Today, the specification of an 404 error document in a .htaccess configuration was really kidding. The standard 1und1 error document for 404 page is everything but looking nice. So we are using a custom one which worked perfect until today. Due to a dynamic generated content, some urls with an encoded /-character, which becomes a %2F ended up on the standard 1und1 “404 file not found” error page.
At the end, the reason for this is pretty simple. The apache webserver does not accept urls to have the %2F character in the url. In this case, the 404 page is used even before your .htaccess is evaluated. Unfortunately, the required apache configuration to allow %2F characters in URLs can not be set in the .htaccess within your webspace, but only in the server configuration in http.conf or in a virtual host configuration (http://httpd.apache.org/docs/current/mod/core.html#allowencodedslashes).
At the end, your only way is to ensure that your website does not generate any %2F encoded slashs in your URLs.