I don't know if it's a feature or not, but when I have a hopper leading into a large chest (it doesnt matter if it's from the top or from sides) the hopper takes the chest as two different chests and when I have an item in the bottom half, the hopper doesn't see it and stores the same item in the top half.

Steps to replicate:
1. Create a double chest and place hopper on top/on sides leading into said chest.

2. Place an item into the bottom half of the chest (I used rotten flesh since I found this in my zombie xp farm in hardcore mode and replicated it in creative to see if it happens with the hopper on the side)

3. Throw the same item into the hopper and wait for it to be transferred into the chest.