What MEG system is this?
The NAS/RPA/LPA points you placed in the MRI look reasonable, so it means that the issue in on the side of the NAS/RPA/LPA points from the MEG files.
Subject A and B: It could be that the what you see is really the positions of the subjects' head in the MEG. It happens that the people are not positioned properly.
Subject C: The position of the head was not acquired correctly at the time of acquisition.
In both cases, there is nothing you can do to "fix" it.
If the subject's brain was far from the MEG sensors, there is no way to create recordings after acquisiton.
If the positions of the head localization coils were not acquired correctly at the time of the MEG recordings, there is no way to reconstruct this information later.