difficult to answer without showing us log, options used, which website...
could be javascript, in that case continue interrupted download after moifying
scan rules by adding this as last rule:
-*.js
Otherwise could be bad rules, builting javascript inside html (inline js), or
other options bad
inline js can be removed by search and replace, find in files, via notepad++
of all html files you downlaoded for following words
search for: <script
replace with: <!--script

search for: /script>
replace with: /script-->