I use httrack to scan my own pages for broken links.  There is javascript in
those pages which uses an html file name in a cookie check, e.g.:  
document.cookie.indexOf("file32.html");

This seems to cause httrack to look for file32.html in the current directory,
which it cannot find - and thus produces a broken link report.

I'm not sure how you'd change the code for httrack to notice that this isn't a
link.  Perhaps something that recognizes the difference between html and
javascript... or blocking html parsing between <script> and </script>... or
?...

Cheers.