Items are constantly being moved around when not used so eventually a transporter will grab that item to take it somewhere and then you can remove it. I'm planning to fix that to be able to remove even when it's occupied but for now use that workaround.
Cheers!

Just encountered the same issue. The game is essentially unplayable once you make this mistake. I am not buying another 20 rifles to compensate for such a dumb bug. Can't you make the code the same as spawn points, where they bring weapons to spawn points, and take them away when you move those?
Also, when they take away weapons from the item spots, you still cant remove most of them, as it says "Item slot is not empty". Needs to be fixed asap