I think Leo is still trapped in limbo. You never saw them taking the sedatives out of them in the plane, and then later Micahael Caine and Leo just appeared at the house.
Also is it possible there there is only one limbo, and therefore making it possible for Saito and Leo to meet up in limbo?
Another thing is why didn't everyone wake up from the 1st layer when they hit the water. Shouldn't they have woken up on the plane without ever having to swim out of the car?