Loot vanished from ship

I was on a Sloop with a friend and we were working on the legend of the veil quest. During the finale we noticed that on the third fort, the ghostly storage crates vanished when we stepped foot on it to get them. Then after we finished the final fort we noticed that all of our emty chests and 2 storage crates along with a firework crate with 33 fireworks and an empty cannonball crate all disappeared from our ship.
Has anyone come across this before? There was no-one on our ship at all because they would have taken the athena stuff if they were taking stuff. I've never seen a bug like this before. Not long before this we also came across a bunch of gold pouches in the water and a couple of items of loot.