MarkUp.io differentiates the page pins that are placed on a given website based on the URL of that page as well as any associated query string variables.
That said, it's important to note that if your website utilizes canonical URLs, the canonical URL for a given page will take precedence over the typical URL of a given page. If your pins are not saving to the correct pages in your website, you will want to review the canonical URLs applied to each page that you would like to mark up.
For example, let's say that you want to mark up the homepage and ‘contact us’ pages on https://www.example.com.
You create a Website MarkUp for https://www.example.com and add comments to the homepage as well as https://www.example.com/contact-us. If no canonical URLs are used or if they are set up to be unique for both pages, your pins will be saved properly to their respective pages.
Although, if you apply a canonical URL of https://www.example.com to the 'contact us' page, MarkUp will interpret that as the same page as the homepage. This means comments added to 'contact us' will actually be pinned to the home page instead.
With the above in mind, if you notice that pins are not saving to the correct page, please review the canonical URLs that are assigned to those pages to ensure they are unique.