This happened to me [repeatedly] as well if I tried assembling it in the instance.
Leaving the instance and assembling it in town it worked fine. Now I'm on the final boss but that appears to be bugged pretty badly.
In the first stage he'll just repeatedly stop doing anything and allow me to attack him. In phase 2 they must have changed it since the early how-to videos were made. I couldn't hit him at all so I went and watched a few, and it's either broken or not the same thing. But even on regular difficulty I'm not sure it's beatable unless I want to spend an hour on it (without screwing up and dying in that time).