If you summon a minecart riding a minecart then the minecart that is on top of the entity stack is below the one it is riding. This can be best seen if you summon a larger stack of Minecarts, because then the stack sinks falls through the ground until the one that appears on top hits the ground. If you put such a stack on rails, all the minecarts exept two will be decoupled from the rails and be below them. If you make the bottom Minecart in a entity stack of minecarts for excample a chest minecarts it is clearly visible that is is on top.
This bug did not exist in version 1.7.4.