I can't see the listing from this comp, but you have a couple options:
- message the buyer and just mention that the payment came through without the shipping cost, and say you'll ship out as soon as that portion is received.
- ask them which shipping method they prefer, then send an invoice just for the shipping cost. I *think* you should be able to do this, even though they already paid. It would be under "sold items" and "other actions" I believe.
- refund the entire payment, let them know about the weird system blip, and send them a new invoice that reflects the complete total.
Whatever you do, don't ship until you have that payment. Most people understand that there are computer errors from time to time - hopefully it won't be a big deal.