I encountered the problem that when pulling items from furnaces (any kind) with a hopper line, (filled by moving hopper minecart) and under that another hopper line pointing into chests seemingly randomly the downward hopper not always gets prioritised. The issue can be reproduced as shown in the linked video. Sometimes in my farm I had the same setup to produce different behaviours. Sometimes all the items end up in the first chest, but sometimes if the furnaces' number is X then the 1/x ammount of items end up in the second chest (which based on the hopper rules should not happen).

Link to youtube video proof