I've noticed that some lists on our 2013 don't come under lists when using site contents. bit confusing so an example should make it clearer
I have a custom list called projectgate and the URL is https://xxxxxxxxx/projects/1625382710/Lists/Project%20Gate/AllItems.aspx.
notice the lists in the url.
I have another custom list called projectwise that doesn't have lists in the URL https://xxxxxxxxx/projects/1625382710/ProjectWiseProjectLink/AllItems.aspx.
I'm confused.