If you add or change a reference in your library while the Citations window is open, make sure you click Rescan to have those changes reflected in the Citations window and in the formatted paper.
For example, if you typed the citation {Geoffery, 1988} into your paper but forgot to enter the reference in the library, EndNote would list a 0 in the Matches column for that citation on the Citations window. You can leave the Citations window open and enter the Geoffery reference into your library. Bring the Citations window forward and use the Rescan button to recheck the library for matching references. This should change the "0" match to a "1."