I've tried both googling and looking through the forums and while I've found a
similar question here, it received no answers.

I'm fairly sure I'm just missing an obvious thing, but I literally can't
understand what I'm doing wrong.

This is the warning (Only one I get), with the website's link instead of
ExampleSite and initials instead of ES and ProjectName being the actual name I
gave the project.
Warning: store text/html without scan:
D:/ProjectName/ExampleSite.org/ES/home.html



So in reality if I take the website for San Diego Zoo Wildlife Alliance it'll
be this warning;

Warning: store text/html without scan:
D:/ProjectName/sandiegozoowildlifealliance.org/SDZWA/home.html
The actual url for the site is <https://sandiegozoowildlifealliance.org/>



It appears the site I am trying to mirror adds initials, could that be the
problem? If so why? I checked and it seems removing that part sends you to a
log-in page, but otherwise you can access the site as a guest using the link
with the initials.