I had the same problem with fondant cracking. This was my first attempt to making a shoe box cake, that turned out more like a cinderella pillow. I had to take the shoe and place it over the crack in the back part of the cake. This was the first time using fondant and have it crack. Did I roll it too thin or did I put too much icing on the top layer to crumb coat. Fortunately, my customer did not get upset. Plus this happened from moving the cake from one place to another.
..moving to Cake Decorating.
It's hard to tell what exactly happened without more details. It looks to me as if your edges and corners on the cake were rounded before you covered it???? The naked cake needs to be the shape you want your finished cake to be.
How thick did you roll your fondant? It should be no more than 1/4" no less than 1/8", I prefer somewhere in the middle. The layer of buttercream beneath the fondant should be basically just a crumb coat, chilling your cake before covering in fondant will help hold it's shape. I'm not sure how the fondant could have cracked on the top during transport, usually that would happen on the edges or sides. If the tops cracks, I would think that would happen when applying the fondant.
It sounds like the cake itself might have cracked and that split the fondant.
Did you level the cakes? If the bottom part had a rounded top and you put the top part right on top of the cake (no cake board on the top part, I mean) then that could have made the top crack after a while.