Your message is condescending even if you don't mean to be disrespectful, but usually people who start a comment with "without being disrespectful" think it gives them licence to then be disrespectful.

The terms were clear. That is the issue. My T&Cs said "a free stopover is permitted in each direction". That was a condition of sale, I understand it was subject to availability. However there was availability. I'm not "alleging" availability. EK agents told me there WAS availability. Now if that disappeared even while on the phone yes I understand that would have been my problem. Availability is not guaranteed. However the issue is not that availability disappeared while on the phone, but that they wanted to enforce a charge contrary to the T&Cs of my ticket.

Your last sentence I believe is correct. I would have had a valid claim for the excess paid. I made a mistake in not "paying under protest" during the first call. I would have avoided the aggravation and also there is little doubt I would have won this dispute. My claim would not necessarily have been limited to the excess paid.

Anyway Emirates themselves have understood and resolved the situation to my satisfaction now.
They credited me airmiles as a gesture of goodwill and are looking into their system to try to understand why it happened because they agree it shouldn't have done.
I'm not pursuing things with my credit card because I feel I have been listened to and the situation has received an appropriate response.

I'm not sure why so many people are trying to put me down for coming onto a flights forum asking for help with a legitimate problem.
Better not to assume the worst in people or to be condescending. I'm not out to rip off an airline, but I do expect fair treatment in any business transaction.