Whenever items are being acquired through an interface interaction like a chest or dismantling your ship, if the inventory is full, items disappear.
Examples:
- I was looting ruins with nearly full inventory. Opened a chest, clicked "take all". Now the chest is empty and some items from it are nowhere to be found.
- I decided to rebuild my starting ship. I took everything from its cargo leaving a few inventory slots empty, dismantled the ship at wharf. I happened to have just one less inventory slot than needed and now the ropes from ship are nowhere to be found.