I'm not able to reproduce this problem. Please be specific about what you mean by protected content.
If the page or feature instance is protected by roles then they should not appear in search results since the allowed roles are included in the search index and used to filter the search results.
If the page is marked as not included in the menu or hide form authenticated, that is not protected content because those ar enot security features they are only cosmetic settings.
If the content is really protected by roles and is appearing to unauthenticated users in the search results then probably something happended to the file system permissions that is preventing the index from being updated when roles permissions are changed. I would try rebuilding the index and make sure the files disappear from the index folder and then re-appear after they are re-indexed.
I also do not know what you mean by "marked list" and "missed markers", those are not terms I'm familiar with so please clarify what you mean by that.