Man that sucks.
Never order from N scale supply without calling first, they're webstock is one of the worst (I don't think they even bother). I've had a chance to interact with them at a couple Denver shows and have not been impressed so far. But I digress.
Microscale is pretty receptive to inquiries about their products. I'd let them know what's going on between the website and the invoice. I've heard that people have been able to get the artwork printed from another vendor as well.
Jason