Having vertices outside the inner skull surface is a problem for OpenMEEG.
https://neuroimage.usc.edu/brainstorm/Tutorials/TutBem#Warning:_Dipoles_outside
You can either force the vertices of the cortex surface to be inside the inner skull: see function tess_force_envelope.m
Or you can recompute another set of BEM surfaces with Brainstorm, using a higher number of vertices.
If you are using @christianoreilly 's templates, I guess the BEM surfaces were created using a different algorithm, probably MNE's mne_watershed. @christianoreilly Is this correct?
Recomputing the BEM surfaces in a different way (as in the beginning of the BEM tutorial) might solve your problems.