I appreciate if you don't want to give details, but it will hinder the advice you will get on here - but I am still unclear on the reason that the agent requested a visa and why you believe one wasn't required? I assume the situation was a bit more complicated than a trip ending in GVA and the passengers having a CH passport for example?

Did you make the booking with BA or with AA?

What is the situation now? Are they still in Mexico or have they booked some alternative route to GVA?