Except if EVERYTHING is misaligned the same way, then they still line up. The Tokamak does not care about the blueprint. The BP is not part of the reactor. As I said, as far as the image is concerned, this appears to be a case of sticking the BP on top of the solenoid, instead of underneath it, not actually having the pieces misaligned.
There's a number of reason why the plasma could be going out like that. For example, if there is a misaligned toroid in the NE section, it will prevent the hasSolenoid flag being set true for the toroids in the image. If the solenoid doesn't have the minimum power, that would also cause this issue. If there is a problem with the LN2 getting into the toroid, that would also cause the plasma to spew out. ( That appears to be a magic wanded reservoir, so that should be fine. ) Lack of charge would also cause this issue. ( I see the lightning crossing, so it's getting charge fine. ) Depending on the order things were placed/turned on, the toroid may just need to be updated. Rotating it 360 degrees will do this.