I would think that any leak causing this would come from the nearby window. I suppose that a roof side seam at the awning could run water down, around the window frame and run across the floor on the underneath side, but that seem unlikely. If the hatch seal was leaking, you could see that evidence. It is odd that it is a small spot without damage leading to a wall. Just thinking out loud, but maybe it is a material defect and nothing to worry about.
BTW, I had that year and model and I strengthened the bed pedestal by building a divider wall at about the middle. It gives you a clean storage area accessible from the inside of the trailer also.
Was 2015 SLX 195RB
Now Bullet 248RKS
2014 Ford F150 3.5L Ecoboost