If you are using a Word document which has citations inside of text boxes, EndNote formats the citations appearing in text boxes first. This means that your in-text citations do not begin with 1. The suggested workaround for this is to convert the text boxes to frames.
Right click on the text box which contains the citation and choose ‘Format’, then ‘Text Box’. Select the Text Box tab and click ‘Convert to Frame’, then click ‘OK’ to confirm the conversion. Now format the bibliography, this should solve the problem.