Hopper doesnt always put items into the container it is "Connected" to

Confirmed. I wanted to do a sorting system. I stacked 5 chests on top of each other with hoppers on top of each other but connected to the adjacent chest. When you drop an item it checks the first chest to try and place the item (sometimes..not always) and if it can't be placed it drops to the last hopper and doesn't even check the other chests.

That's because the hopper below is pulling items out of the inventory of whatever's above it (in this case the hopper above it), not because the hopper above is putting items into the hopper below. To me, this seems more like intended behavior than a bug, and I believe they intend to modify the hopper system so players have more control over when a hopper takes items and when it gives items, and that's part of the reason that the hopper is marked a 'work in progress.'

From how I see it Mojang can only fix this efficiently by adding a pipe system for the hoppers. Otherwise we just have to avoid using compact designs.

This ticket has been marked as a duplicate of MC-6162, in favor of the better description/information provided.