This might be intended behaviour, however I think it doesn't make sense.
When you have a belt that drops off items to another belt, the belt graphic looks like it is above the next belt, however the item, which would be below that belt is not obstructed (in technical terms the z-index of items is too high).
Since it is only a small part of the item that would be obstructed, I think this is a bug and not intentional. In my opinion it looks "wrong" and hiding such a small part of the item sprite would not hurt. Other buildings can obstruct items too.
Congratz to the 1.0 release by the way, Factorio is my all-time- favourite game
