I think I've identified why it's trying to set a duplicate signal now at least.
If there are two sections with the same item signal (however it got into that state), the sorting logic will set them each in turn into a new empty slot. This will of course fail on the second one because it was set in a different slot previously. So the code needs to be updated to probably just overwrite the previous signal of the same kind (so if the combinator being built somehow has two sections with a coal signal, the last one processed will "win").
Will have to wait until I get home to actually be able to verify the fix though. Also, what do you mean by "transportation tab(the car)"? (Edit: Oh of course, the transport category in the inventory.)