So, yeah, a manufacturer tried to game the certification process to save a few bucks (and months) on a new aircraft design. That's a failure. But it's not an unforseen one!
The safety value for manufacturer shenannigans is supposed to have been the certification process itself. And I gotta say the worst failings here are with the FAA. At any point someone could have looked at the process and seen:
1. They changed the engine
2. They had to move it because it was too close to the ground, but they couldn't stretch the landing gear and keep the type certification.
3. So they moved the engines forward and up
4. But now the aircraft was less stable, and they couldn't change the tail design and keep the type certification.
5. So they did software-managed stability augmentation instead
6. But (that's right) they couldn't change the autopilot and keep the type certification.
7. So they did it with the trim, which had never operated under autonomous control before.
I'm sure I have a few of those details wrong, but the point is that any bureaucrat familiar with the aircraft could have seen that this was a ridiculous house of cards they were playing with the type certificate. I mean, one change with one workaround, sure. But a cascade like this is just obviously a perversion of the process.
Yet no one said something. Or if they did they were overruled.
The way the built-in incentives work, it's not feasible to rely on 100% forthright and honorable manufacturers. So we have a regulatory body to catch those failures for us, and it failed.