Interesting,
I don't see any particular issue with the save file, perhaps the issue is on save and not on load.
Can you confirm that the issue only happens for Common & Immutable items that are picked up.
The only thing that comes to mind is that the item pickup may have given the item the wrong ID but that shouldn't be happening since the item is registered in Awake.
What script are you using for the pickup, is it an ItemPickup + Item Object or an InventoryPickup + Inventory or something custom?