It wasn't a scam if you got a receipt. It is a legitimate fee that you encountered. But the whole credit terminal not working/must pay cash is fishy for sure. The agent made you pay essentially a penalty for checking in your baggage under the time limit for national flights. "Documentacion Extemporanea" Viva Aerobus Extra Fees
Did you recieve a receipt for your payment? Was it even offered? If you didn't then I would lean towards the fee was kept by the employee.
Like 'jjbiv' mentioned above, you need to report the experience if you weren't given a receipt or cannot see the fee within your reservation details.