You were probably the only ones with reserved seats on that train. Seat reservations are not needed on Swiss domestic trains. You were expected to do what everyone does: Just get on board, and find yourself seats to your liking.
It is unfortunate that you did not know this, but that is how trains work here. Trains are mass transit, used by people to go about their daily business, and as long as the train operates and is on time we consider the service as expected.
The staff member that spoke to you was probably surprised by your request, and hence may indeed not have given the answer you expected.
That said, you should request a refund of your reservation. Start here:
https://www.sbb.ch/en/help-and-contact/refunds-compensation/refunds-compensation.html