Steps to reproduce the issue

Turn on SEF in Backend and create (with JCE-Editor) a link to an article that is not linked in any menu. In my case I got:

index.php?option=com_content&view=article&id=677:gespraechsforum-handy-in-der-schule&catid=261:medienbildung&Itemid=472

(Where the appended Itemid 472 is the one of the main menu which is okay for me.)

Expected result

I am expecting a SEF url that points to the selected article:

http://www.humboldtschule-berlin.de/261-humboldt-gymnasium/profil/medienbildung/677-gespraechsforum-handy-in-der-schule

Actual result

I got the right url, but all slashes after the hostname-part are missing:

http://www.humboldtschule-berlin.de/261-humboldt-gymnasiumprofilmedienbildung677-gespraechsforum-handy-in-der-schule

System information (as much as possible)

Joomla! 3.5.1 Stable [ Unicorn ] 05-April-2016 22:45 GMT
Joomla Platform 13.1.0 Stable [ Curiosity ] 24-Apr-2013 00:00 GMT
PHP 5.4.45-0+deb7u3
Apache

Additional comments

Adding the following 3 lines before the return-statement in the build-function of the ContentRouter-class (in the file ./components/com_content/router.php) fixed the problem for me, but I am pretty shure that this is not the right solution:

for($i=0;$i<count($segments)-1;$i++) {
   if(strlen($segments[$i])>0) $segments[$i] = $segments[$i]."/";
}