Minecart with Hopper/Chest stealing items

So I am in the process of making a working city with power, water etc.. I made this tree farm where when you cut down the trees, the wood, saplings and apples go through a minecart which drops them into hoppers that puts it into furnaces. No matter if I used a minecart w/ chest/hopper, it didn't do what it's intended to. It stole the items from me. If you use a minecart w/ chest with a stack of wood in it, it comes out as a stack of 34 and a stack of 1 wood still in the chest.

Steps to reproduce: Setup a rail with hoppers below it going into furnaces.