Snapshot not picking up new articles in SQL Server 2012 transaction replication when added through script
Maybe Brandon's idea here will help:
How to add an article to existing replication

Summary of his suggestions to fix:


execute sp_refreshsubscriptions for pull subscriptions  
or in push subscriptions use the sp_addsubscription as you mentioned (worked
for me)


I wrote some code to help identify the "orphaned articles on subscriber's":

--Run from distributor
SELECT  pub.data_source AS Publisher ,
        a.Publisher_db ,
        p.Publication ,
        sub.data_source AS Subscriber ,
        s.Subscriber_db ,
        a.Article
FROM   distribution.dbo.MSarticles as a
LEFT JOIN distribution.dbo.MSpublications AS p ON a.publisher_id = p.publisher_id AND a.publication_id = p.publication_id
JOIN sys.servers AS pub ON p.publisher_id = pub.server_id
LEFT JOIN distribution.dbo.MSsubscriptions AS s ON a.publisher_id = s.publisher_id AND a.publication_id = s.publication_id AND a.article_id = s.article_id
LEFT JOIN sys.servers AS sub ON s.subscriber_id = sub.server_id
WHERE s.subscriber_db IS NULL --Leave off for great documentation, but this will show the "orphaned" subscribers effected by this issue.