We have always stressed the importance of checking a few of the manual steps in the beamforming processing stream where possible.
These include the outputs generated by the co-registration routines which co-register your MEG headshape to your structural MRI for each subject, and simultaneously calculate the local sphere sources for each channel in the MEG sensor array. This information, calculated early in the processing tree is obviously vital for all post-processing steps.
You should be routinely checking that the co-registration itself is accurate and that the spheres generated make are 'sensible' for each sensor.
If you are not doing this you are STRONGLY ENCOURAGED to do so. Whilst there have been very few instances of the outputs failing (only 2 in the last year!) they have had significant effects on results for both individuals and groups.
These errors are easily resolved if detected.
Please see the following page for more information:
https://www.ynic.york.ac.uk/doc/BeamformerUsage and see "/STEP 3 - Visually check that the co-registration is reasonable for each subject and associated MEG run/"
(Thanks to those who brought this to our attention!)