Well I am running httrack to download interactive stories, all links are in
.html, however I have noticed httrack seems to be downloading links to other
stores as well.

I have entered the URL of the story I wish to download, something like:
storys/interactives/865379/Story-name/ (not a real link)
Now I had set httrack only download links from under the URL, sadly that
didn't seem to be so.

I was hoping someone might help?
More details:
Preferences and mirror options:
Under Tabs:
Links
Get HTML files first! (only selected)

Build
Local Structure: Site-structure (default)
No Error pages
No external pages

Spider
Accept cookies
Check document type: if unknown (except /)
Parse java files
Spider: no robots.txt rules
Update hack
URL hacks

That's all the settings, anything left out was unticked.