Copying and merging some pages and documents may not work correctly when the positioning of shapes on a page is under the control of Visio or an add-on within Visio. Various of the built-in diagram types within Visio are of this type:
Shape position, shape name, connections and other factors can all be under the control of Visio, so copying a diagram may result in anything from small imperfections to a total mess. There is nothing that can be done about this.