Check everywhere well
The Last of Us 2 has a large map, which means that there is plenty of space to hide various objects.
Objects play a very important role in upgrading Ellie and her gear. Search all the places and corners to find different objects. Even the desks you need to upgrade your weapons may be hidden.
Do not leave the area at all until you are sure it is empty. Rattle all the doors, break all the windows and check around all the corners.
