I guess it is just a general bug, that the chest spawns do not take their surroundings into account.
I have already encountered quite a number of chest hidden in walls and floors. I guess that has always been the case, but only with the new passive from Greymore last year you can actually see them.
So with your underwater chest it is probably the same thing, but instead of inside a wall it landed inside a lake.
There's one way in the south of Bangkorai, near the instance entrance stuck in an L of rocks, its facing inwards so no matter where you position around the chest it can never be in range and perpetually stuck there for all eternity.
There is one in N. Elsweyr; it is below the surface of ground. If you have the Keen Eye: treasure chest passive from Excavation, you can see it, otherwise it is invisible. If you position just right you can open it.