Young Joe falls from the ladder. The next scene is a flashback. Read about that here. We then see the events the led Bruce Willis to coming back in time without a hood on, his escape from Young Joe/JGL, and what he was doing while JGL was in the apartment trying to get the silver and run. It turns out Bruce Willis wasn't far. Which is why we see Bruce Willis watch JGL fall from the fire escape and onto the car. JGL isn't dead. He is unconscious. Willis drags the unconscious body to the train tracks, hoping JGL will get on a train and continue on with his life. Obviously this doesn't happen.
To be clear: Young Joe only dies once in this movie, and that's when he shoots himself. The fall does not kill him.