Are you sure that the document itself is using APA 6th? It sounds like it may be using an output style that depends on Footnotes?
Try switching to another output style – Like Numbered or Annotated? do the citations now get numbered, for numbered or (author,year) for annotatedand a list of references appear at the end?
Then try switching the word document output style back to APA 6th? You might also want to download a new version of APA 6th from the Endnote: help dropdown, webstyles finder, incase it got corrupted somehow?