Symptoms

Both sites > Lists will have artifacts from each of the lists, ie look like duplicates.
 

Diagnoses

Duplicate Artifacts in List after appifying in scenario where you have 2 sites with same TITLE and identical list.

IE - Mysite TITLE with site URL https://someplace.com/sites/mysite1
MySite TITLE with site URL https://someplace.com/sites/mysite2

SP allows for Sites with same TITLE aslong as site URL is Unique.

Cause: when you appify the list called List1 on the first site it created the category and adds all the artifacts to the category. then if you go to site 2 and appify the list called List 1 and the title is used for the category name the category already exist and the artifacts is added to the previously created category. looking like dups but essentially pointing to different site URL's but ultimately in one category so both sites lists will have same artifacts due to the "shared" category

 

Resolution

Logged as a bug.
We cleaned all artifacts from both sites and then deleted the sites, recreating the sited with unique titles and deployed the package to them.