Create an item elevator (as shown in the uploaded picture).
Build a hopper chain with a dropper on it through the item elevator (also as shown in the picture).
Put items in the bottom chest, place yourself at the top of the item elevator. You will receive less items than you put in the chest and all containers will be empty.
Not sure if this helps, but sometimes you can see the top of an item entity in the dropper (it is a full block, so the item entity apperars dark) and it will disappear under your feet. So I think the items are deleted in the dropper block.
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Wow, I did not check the hopper cup, that was dumb. I once tore down the whole thing but the items must have despawned in the meantime.
The reason I put a dropper there was to check if an item elevator could be intersected by a hopper line (might be useful if you don't have a lot of space) and I like to experiment with redstone stuff.
Ilmango and MethodZz built this and analyzed it. This is pretty wild and an interesting find. Unfortunately, we don't think this is a bug.
The way to see what's happening is to place a redstone block next to that hopper in the middle, locking the hopper. Send items through, and when you break the dropper, you'll see the items you lost just sitting there in the indentation of the hopper.
Why the items get lost is that hoppers with containers on top only check the container, not the airspace above the hopper. So your lost items are sitting in the indentation of hopper and not getting picked up.
We could argue about how we feel about hopper cups and how things get stuck in them. It's pretty annoying. I don't get why hoppers have to have these indentations, but this is obviously intended behavior. To fix what you're seeing, the hopper hitbox would have to change, at least temporarily if a container is on top. I doubt that would be implemented, although we can let the devs decide.
Meanwhile, since you know the cause, you just know that you can't have a hopper in the middle of an item elevator with a container right on top and have it be reliable. Why did you put a dropper there in the first place?