This may help. From my experience...

You should check that file manually, is it exist or not. (HTT really
'sometimes' missing some file with randomness.)
Also you should test with simple link as WHRoeder suggest. If it's script link
it maybe because the script is too complicate that you didn't download all
required script (external source etc.).

And from my experience. After the 1st times of download HTT if you
download/update again it often drop local reference to global instead. At
first I deal with it with download from scratch (Dont know why but I must
remove all old file. Otherwise, it's not Local Ref#). But now I use GM script
to change path to Local instead. So I dont care about it now.

In sum, if you test it with offline. Try to online while testing. In case that
Local Ref# broke somewhere to Global it'll work.

Usual I found these cases:
1. Missing page
- From your post "that maybe don't get processed and downloaded by httrack" ->
You can just check it easily to cut it off the case or knowing that it's the
root of problem.
2. Missing script (Rarely case because I usual do as 5)'s of  	WHRoeder)
3. Global Ref file while we have a Local one.