Money charged but iPad waitlisted, yet Apple Pencil is already shipped

I ordered an iPad with an Apple Pencil. Where I live, students get the pencil for free during summer break, so I only paid for the iPad (pencil was included!). The money was deducted from my card, which was the price for the iPad (789 euros), but a bit later Apple tried charging my card for the Apple pencil as well (139 euros). Please keep in mind, the final price i had to pay was 789 euros (for the iPad only), which is now not on my card anymore. But here's the thing, the Apple pencil is already shipped and on its way, but Apple is saying that they have not received the payment for the iPad yet, even though i very much have already paid for it. So now my iPad has been 'waitlisted'. I don't know what to do now, it's all so confusing. Could it be that the payment is still processing on my card's side? Should I wait for a day or two, or should I contact Apple?