You can find a detailed invoice in Mijn NS (the website, not the app; go to Betaaloverzicht/My payments) to see what you are being charged for. Perhaps some correction fees are applied.
If after looking at the invoice you still feel that you are being charged too much, or if you can't find the detailed invoice, then you should contact customer service directly. They can tell you what the higher amount is for, and correct an incorrect invoice.
Usually, contacting customer service this is most easily done by phone, as they are available 24/7 at 030-751 51 55. You may also contact them by chat (click the link Chat with NS on this page) or by sending a message on Twitter or Facebook.
It could be that the travels were from the previous month. With NS Flex it can sometimes take longer for travels to be available in the travel history. Usually it is a few days but it could also take a few weeks. When it takes longer for travels to be available in the travel history, it could also be they are invoiced a month later. You can compare the invoice for this month with the one for the previous month and your travel history to see if this is the case.