MarkUp differentiates the pages pins are placed on in 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 precedent 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 home page and contact us page on https://www.example.com.
You create a MarkUp for https://www.example.com and add comments to the home page 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. If you apply a canonical URL of https://www.example.com to the contact us page though, MarkUp will interpret that as the same page as the home page and comments added to the 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.