Indeed.
If that was the case then as above the TA should have advised options, rather than proceeding with something that explicitly violated clear written instructions from the customer. Whether there weren't eligible fares is immaterial.
This is a very simple issue, which is easy to look at objectively if you ignore the fact that it involves a TA.
A business was given a clear instruction in writing. If it did not understand how to fulfil the instruction, or was otherwise unable to fulfil the instruction, it should have advised the customer so further discussion could take place. Simple as that.
As consumers, we're in for a world of misery if businesses aren't held to that absolutely basic standard.
The OP is probably in a relatively good position given the written instruction. Judging by the experiences of a TA I know (including when the customer is in the wrong), if necessary the threat of escalation to management or fair trading will probably secure an outcome.