Steps to reproduce

Let's first visualize the magnetometer channel positions via Raw.plot_sensors():

import mne
from mne.datasets import sample


data_path = sample.data_path()
fname = data_path + '/MEG/sample/sample_audvis_raw.fif'
raw = mne.io.read_raw_fif(fname)
raw.plot_sensors(ch_type='mag')

This produces:

Looking good. Now let's plot PSDs of the data.

raw.plot_psd()

Result cropped so it only shows the sensor positions (top to bottom: mag, grad, eeg):

The magnetometer sensor layout looks incorrect, and doesn't match the one produced by plot_sensors(). Am I missing something here?

cc @agramfort