In a single session today, about 15 chests were lost from ships I sunk, as they too sunk below and I was unable to pick them up. I haven't seen this until today. I swam to the bottom as far as I could to search for the chest hitboxes.
I'm assuming this is unintentional, in which case it is a very catastrophic bug to the core of the game, and should be a top priority.
