ID is telling you that you have pages with the same number assigned in more than one section, and that the numbering style is the same, so the program cannot distinguish which one you might mean when you tell it do do something that requires knowing a page location, such as moving pages or printig a page range.
You correct the problem by changing the numbering style for the section, by using small roman mumerals, for example, for front matter and arabic numerals for the body of a book.
Sorry, didn't look closely enough. Changing number style may fix it, but it looks to me like that warning says you used the same section prefix (or didn't sue a prefix at all) on multiple sections, and those sections also have pages with the same numbers. ID defaults to using a section number as the prefix, Did you change that?