• "Most Visited" and "Recently Bookmarked" are examples of the so called Smart Bookmarks folders and are not real existing folders.
• Such smart folders show a list created by a query of the places.sqlite database that stores the bookmarks and the history in Firefox.
• Smart folder lists show a maximum of 10 entries by default.
• Bookmarks that show up in a smart folder list are stored elsewhere in another folder and any changes made are applied to the real bookmark or history item.
• If you remove an entry then the list is shifted up and a new entry that wasn't shown previously is added to show 10 entries.
• If you add a new bookmark or visit a website then a new item is added at the top and the entry at the bottom disappears from that list.
• Items that disappear from the list are not gone, but merely do not show up anymore in that list.
• Actions like copy & paste or delete that you perform on bookmarks in such a list are done on the original bookmark.
• If you do not want a specific list then remove that query (right-click: Delete), but do not delete the content that is displayed in such a list.

I get all of that but it still dosent help me to stop it or see the rest of my list of unseen book marks

Now that you know what you were doing (don;t forget to mark Cor-els as solved)...

You might find working from the bookmarks sidebar ("Ctrl+B") easier to work from, if all of those recently bookmarked pages went into the "Unsorted bookmarks", where they would be added to the end. From there you can move then to folders, delete them or add bookmark separators.

If you copy a bookmark from a smart folder list and paste it elsewhere in an other folder then you create a copy and you have the bookmark in two folders.