As discussed in other threads (but don’t worry, even I have trouble finding them, and I know they are there!) most publishers actually specify the order to be based on alpha (author) then year and then usually title, which is what you are getting, and not in order of citation. That is because in the bibliography itself, that is how they want them to be listed. – but CG provides a solution if you want to override the settings. Here is one of the other threads.
http://community.thomsonreuters.com/t5/EndNote-General/Ambiguous-citations/m-p/29629#M6606