07-12-2017 04:53 PM - edited 07-13-2017 05:36 PM
It is likely it is still in your manuscript's travelling library. You can only fix that by deleting the formated citation itself, or by converting all citations to unformated citations and then reformating by updating the citations and bibliography. When you do so, endnote will query that citation as it is no longer in the library.
added in edit
or by right clicking, edit citation, more and finding it in the list and removing it there.