The new search bar that appeared today looks great but I'm not sure how to get the search results as it previously worked for lists and libraries. Is there a new setting? It appears to be looking for files in OneDrive if anything. Any help on where to find settings, why it is defaulting like this, and how to fix it would be greatly appreciated.
As mentioned in my comments above, this is part of a new feature rolled out by Microsoft in your tenant. Please check this link for details.
Basically, Microsoft is trying to provide uniform search experience on their Office 365 suite of products and this feature is now slowly rolling out to tenants. If you create a new Office 365 environment right now, this feature would be available.
This search bar, although is positioned differently, should work similar to before. Please remember, this is contextual search, i.e. the search will happen in the scope you are within. If you search from the home page, then it will search entire site, if you search from a document library, then it will search only that document library.
You will get similar experience if you go to Office search.