So, looking through the errors and the logic, this narrows down to two possibilities:
- some really weird items that do not have prototypes (unlikely)
- some non-item/non-fluid signals that are present and interpreted as items
I pushed 2.1.1 which hardens the signal handling (basically ignore anything that is not either a virtual signal that controls LTN, an item or a fluid signal). This should make the second option go away.
If you still encounter problems with the 2.1.1 release, to be able to figure out the problem, I need
- the stack trace
- a game save (that is ideal but I understand if you don't have one). Send as a PM or a file share through the forum messaging.
- what you were trying to ship
- a list of mods that you have loaded in the game. Especially unusual mods or mods that change items and/or fluids around.