There are multiple locations that the Alma Doll may appear on each level. Restarting the mission will change the doll spawn.
After you exit the cafeteria, there is a staircase with bars in the middle. At the bottom of the stairs is a locked door to the left that you can shoot open and go further down the stairs. At the bottom you can crouch under the stairs to get the Alma Doll.
Location A: In the room with the hole in the wall right before the mech section, you may find the doll to the right.
Location B: After you kill the mech there is an opening across the street from the building with rockets in it. It is in the second floor, you may find the doll here.
The second time you are in the warehouse, climbing shelves (after the bathrooms) climb to the top of the shelf. You should see the Alma Doll on top of another shelf with a crooked ladder leading to it. You have to sprint along the edge and jump to the crooked ladder to get to it.
It is right behind the Mech suit, under the basketball hoop.
On a second play through, it is in a room on the second story of one of the buildings.
After you see the helicopter crash, jump into the subway car in front of you and take a left into another subway car. The Alma Doll is in this subway car to the left.