Welcome to the NS Community!
Something probably went wrong when loading balance in Amersfoort. After the payment you need to present your card again to load the balance on your card.
If you didn’t do that (or something else went wrong), the money will be billed back to your bank or credit card within a few days.
Welcome to the Community.
Can I ask wether you were able to check-in at all from Amersfoort? And wether you were using an Anonymous Card or one on Name?
NS usually prevents you early on from Check-in if you don’t have enough money on the card, so it’ll be weird if it only stops you at check-out with an anonymous card.
Do you use any discount subscriptions and did you at any point switch from Transit Company or had to check-in and -out at a station to switch from platform? I highly doubt that you could’ve missed the second scan as the machine makes annoying sounds to remind you to rescan your card after payment.
As long as you have your payment, you’ll also have proof of payment, just got to be sure it’s on the right card aswell.
The full-fare price for Amersfoort to Rotterdam Alexander is € 14,50 but € 16,00 is needed when checking in (€ 20,00 will be withheld from your balance).
You probably checked in at Amersfoort Centraal through a Connexxion gate and not NS.
See https://www.uitcheckgemist.nl/?locale=en for a missed check-out with Connexxion and fill in Amersfoort - Amersfoort and you will get the € 20,00 back.
For the NS part (which probably cost you € 20,00 as well, so you can get € 5,50 back), contact NS Customer Service (phone, chat, social media).
