As a qualified accountant, I agree.
The laws surrounding trusts can be very nuanced which your standard conveyancing solicitor would not understand. It says a lot that it's taken high level tax specialists to come to the conclusion that the additional rate applied.
I am not a labour fan, or a labour voter, but I can see how a mistake on this can be easily made.
If you use the HMRC stamp duty calculator, the question of "will the purchase of the property result in owning two or more properties". She doesn't own two properties, so the answer to that question is no.
The next question is "have you ever owned or part owned another property" and says you should say yes if you "are a beneficiary of a trust that owns a property". But that question is there to determine if the first time buyer rules apply, not the additional levy.
Based on HMRC's own calculator, it says the additional amount is not due.
This level of tax knowledge is well above what the regular person should be aware of.
If I were AR, I'd be looking at the firm that set up the trust, rather than the firm that did the conveyancing for her new flat. The firm that set up the trust should have been aware of the implications for any new property purchase.