I suspect that the document has “unlinked” some citations from the existing library and they are in the “traveling library” embedded in the document. You should be able to (make a copy of the document for safekeeping first) - convert to unformated citations, then update – which should get rid of and relink any of the citations to the one in your library which will be correctly categorized? I don’t know if that complicates matters, as I don’t really use the categorization tools.