For Cookie Scanner to work properly the site should be publicly accessible, otherwise the scanner can’t access the website.
The Cookie scanner is mimicking the site’s user, which is surfing the website.
What the user is doing, accessing, or loading in the site will affect the amount of cookies that are in the site.
In these rare situations, cookie scanner cannot detect the cookie, for example:
A particular cookie is added not on page load, but later.
A particular cookie is added after user somehow interact with the site (clicking on the link, submitting the form, etc).
To learn more about how to block cookies, read this part of the documentation.