From the image it is only visible that some input products and output waste flows are not connected (the red dots, e.g. Water), this only leads to incomplete supply chains and still allows a calculation, and is not linked to an unconnected graph.
It is possible that you have "somewhere else" in the model graph an unconnected process, visible maybe if you zoom out.
Btw, you can see all processes linked in a product system with this script (so all processes except the reference process, usage in your case; paste the UUID of your product system in the script):
select name, ref_id from tbl_processes where id in
(select f_provider from tbl_process_links where f_product_system =
(select id from tbl_product_systems where ref_id = 'ADD_HERE_YOUR_PRODUCTSYSTEM_UUID'))
(execute in the sql window)
Be aware that if you have many processes in your product system, this will take long as the query is not optimised, but your system seems small.
