You say you’ve “copied and pasted the URL as usual when entering the reference” – presumably in the Endnote record’s “URL” field. It’s unclear to me, however, whether you deleted the “http” prefix from the record’s URL field after pasting. (You could also use Endnote’s “Find and Replace” feature to delete the “http” prefix within the URL field from all records. As a precaution make a backup copy of your Library before proceeding.)
Deleting the “http” prefix from the Endnote record’s URL field should prevent it from being displayed in the bibliography. If it is being displayed for a random number of references, recheck the corresponding URL field in the Endnote record. If there is an “http” prefix then delete it; if there isn’t then delete the entire field to clear it then reenter the web address again and save the record.
If you continue to experience issues suggest you contact tech support: http://endnote.com/support