Since 1.8.2 pre4 hoppers grab items from above from minecarts, that are standing on the block next to the hopper. This doesn't affect all directions. When the minecart is facing towards negative z or negative x, items remain in the minecart. In all other direction the hopper grabs the items. This behaviour was different in older versions.
Players can deal with it. But at least it should be consistent in all directions. Orientation related behaviour is really annoying in Minecraft.
I also uploaded a video, to demonstrate this behaviour
I'd just like to mention that this problem seems to still exist on Realms servers in 1.8.3 for whatever reason. I observed this when I updated to 1.8.3 and my super smelter didn't work, and I was able to narrow the problem down to this. My hopper lines are one full block apart and the items still distribute from the one line to the other.