Couldn't replicate the incorrect destination issue you described, but the game doesn't (yet) explain how that system works either. The colour of the flag in the top left corner of the blueprints denote which shipping route that particular ship/train/etc. is going on -- you can flip through all the current blueprints with the dog-eared button on the bottom right of the shipping menu to find the right route for a particular parcel. Hope that helps!
Successful ending should be possible now! We bugged it out when implementing endless mode :(