popup is supposed to be shown only temporarily while you are in the editor and if your cursor is position on the link. There is some serious issue if you get it all the time on the screen and it does not go away if you refresh the page and change the position of the cursor. Could be that there was some error on the page and when you saved the content it saved it together with opened links.
It is hard to say, I would need access to that chapter or see raw HTML of the chapter to figure (viewable with "Edit Raw HTML" option in the Menu) what is going on.