What makes the mannequins different from the results of the sacrifices' human transmutation attempts?
It's very simple. The so called act of "human transmutation" means that the intent of such alchemy is to create a fully functional human being, complete with memories, emotions, capability to feel and think. In other words, a perfect copy of a person.

The mannequins are mere cannon fodder. They don't have the ability to feel or have complex thoughts. They are just war machines following the order. That was the original intent with which they were created.

Compared to transmuted people, mannequins are much simpler, and as a result pose a much lesser threat to the world. Imagine if human transmutation went perfectly every time, and that you could create any number of smart, ingenuous people. What would bad alchemists do? Recreate evil geniuses of the past maybe, which would be much more dangerous than a bunch of brainless soldier mannequins. That's one of the reasons why human transmutation is forbidden, aside from being impossible to perform perfectly.