Perhaps I don't understand, but I've seen the looping error on the new versions
of httrack and have gone back to using v 3.33.  That seemed to eliminate the
looping error.

I think that httrack can only follow html links within files.  It does not
grab contents of directories - unless all the files in the directory are
linked from an html document.  I don't know which site you are trying to
mirror, but you should start from the html file which contains the links to
the pdf.  I mirror a government site weekly which is made using "plone," a CMS
system, and it works fine for me.  There are many pdf files in the mirror.

Anyway, the first thing that I would do in your shoes is install httrack 3.33
and try again, with the html file as your starting url.