I attached a Trawl Net to my Cargo Ship and started catching things in it. It soon got full and automatically detached. I rowed over to it, opened it and hovered my mouse cursor over each item and pressing the Change Box key, which were mostly Jellyfish (and 1 coral, 1 stone and 1 mussels, I think).
On the first 6 or 7 items it worked as intended, adding the items to my Cargo Ship's inventory. But on the (I think) second-to-last Jellyfish, pressing the Change Box key twice seemed to make 2 more jellyfish spawn in the water next to the Net while the ones in it did not disappear. Upon pressing it again (I think) a 3rd time, the Jellyfish I'd clicked on got its green freshness indicator replaced with a percentage and the game immediately crashed to desktop. The percentage was different each time I reproduced the bug: 87%, 67%, 97%.
I tried retrieving the items with the mouse after my Ship's inventory was full and it worked as expected, without bugs or crashing, so I'm pretty confident the issue happens when you use Change Box while having no space left in your Cargo Ship's inventory. But I didn't test whether it happened without a Trawl Net or without a Jellyfish.