The bug

Hoppers do not properly iterate through chest-minecarts or hopper-minecarts when trying to transfer items into or out of them. Instead, they select a random minecart each tick. Due to this, item transfer takes longer than expected.

How to reproduce

Place a hopper with a rail on top. Place multiple chest minecarts on the rail, a dozen or so. Place items in a single minecart. Notice how they flow much slower than the typical 2.5 items/s.

Code analysis

The following is from version 1.12 MCP 940, in net.minecraft.tileEntity.TileEntityHopper, in the method getInventoryAtPosition:

if (iinventory == null)
{
    List<Entity> list = worldIn.getEntitiesInAABBexcluding((Entity)null, new AxisAlignedBB(x - 0.5D, y - 0.5D, z - 0.5D, x + 0.5D, y + 0.5D, z + 0.5D), EntitySelectors.HAS_INVENTORY);
    if (!list.isEmpty())
    {
        iinventory = (IInventory)list.get(worldIn.rand.nextInt(list.size()));
    }
}

The hopper randomly selects one of the inventories from the list, causing the bug. A fix would be to select the first non-full inventory for pushing items, and the first non-empty inventory for sucking items.