It's hard to understand what I mean without showing it. I know I wouldn't from my own description. So here's what I mean:
Is basically this, a sideways turret:
So when you make a codeRed animation, you animate the piece of the ship and the whole turret, so two rotations in total, like this:
But you animate the joint that is parent to the whole turret, not pieces inside the turret, the whole turret mount.
So wings have upside down turrets:
So if in the codeRed animation you rotate the whole turret, it looks like this:
This is how would it looked if you didn't animate anything:
If you were to animate the rotation of the whole turret in yet another axis, a second one, you could, but then it would do this:
The gun would dislocate from its joint.
You could solve it if you could animate the inners of the turret hierarchy. But I don't think that you can.