Not sure what you are getting at. First of all, both of those statements are wrong. A Primary Key is required, not just an index (although a primary key is enforced with an index). Table structures do not have to be the same, they can be different; i.e. I can choose which columns to replicate as long as the key columns are replicated.

Replication is set up at the database level. You can choose which articles to publish (tables, views, stored procs, functions...), but you cannot set up 1 publication to replicate tables from 2 different databases.

Nevertheless, none of your points address the OP's issue. So, to the OP... You are going to want to double-check the settings on that one publication. I have found that sometimes it is just easier to delete the subscription, delete the publication, and then do it all over again. However, that will depend on how big your db is and how the business tolerates the subscription being down for a bit.