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Groningen - Winschoten is served by Arriva, so it’s likely that you checked in with NS in Groningen.
You can contact NS Customer service (phone, chat) and tell them you did not travel with them, to get the €20 boarding fee back.
For Arriva, wait until tomorrow and see www.uitcheckgemist.nl to correct any check-in at Winschoten, then fill in Groningen as the departure station (which will be listed as destination because you checked IN at Winschoten). You will then get another 12 euro back but if you didn’t top up and check out in Winschoten you will see no missing transactions.
Then I checked in at 16:34 (I received a notification from NS app about check in) and got on the train.
After arriving at my destination I wanted to check out in Winschoten train station but it said that I need to top up my balance. So I decided to check my balance at the machine and it said that 20€ were withdrew from my account at 16:34 (the time i checked in).
Why did it do this and can I get my money back?
Trains between Groningen and Winschoten are not ran by NS but by Arriva. You should therefore have in Groningen checked in at a red Arriva pole and not at a yellow NS pole.
The rules are simple: you always have to check in and out at a pole of the traincompany you are travelling with.
You can best contact customer service of both NS and Artiva in order to get this corrected.
At which check-in pole did you check in at the Groningen station? Trains to Winschoten are from Arriva. So you should check in at an Arriva pole. If by mistake you checked in at a NS pole you had no valid ticket for the Arriva train and what you thought was a check-out in Winschoten wat actually a check-in for Arriva. And since you did not check-out at a NS pole there was no boarding from NS returned. Check you transacations to see if this is the case and if so contact the NS customer service.