Having a hopper with all slots containing the same items will not pick up that same item if there is a different item sitting next to it.
1. Place down a hopper.
2. Put a slab on top of the hopper.
3. Put 5 of the same items in each slot of the hopper.
4. Drop a different item onto the slab/hopper.
5. Now drop the first item onto the slab/hopper. It will not be picked up even though it is the same item as the ones in the hopper.
This also happens with hopper minecarts.