I found this bug when attempting to build a super storage system. When you build a setup like in the attached picture and drop an item into the hopper, the item disappears. It isn't in the hopper (comparator output 0, no items in inventory screen) and it isn't in the Shulker Box. Placing an item into the hopper manually, however, works as normal.
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Just from a redstone perspective; it looks like you have a hopper under the shulker box to pick up the dropped shulker box when full. However, hoppers can also pull items out of containers like shulker boxes and thus will remove the item from the shulker.
Hm, I built your exact setup and can't seem to reproduce. Does this happen every time?