I have had this issue where Endnote was duplicating references as different numbers. It turned out to be the Travelling Library and my Endnote library. To solve this, got to ‘Edit & Manage Citations’ in Word and then any that say ‘Travelling Library’ . There will then be an option (A settings cog on a mac) that gives a dropdown box. Select ‘Update from My Library’ and it will then remove the Travelling Library ref and conform with the numbering form the library inserted reference.