I don't know what is causing this bug. The freesurfer registered are for some reason missing from the anatomy files. However, I will not go further to debug this approach because the mixed head models are really not aimed at working at group level.
We don't have any method for projecting the sources obtained in the subject space to the template space.
I added warnings about this in the documentation, and may move one step further and disable it directly in the code.
https://neuroimage.usc.edu/brainstorm/Tutorials/CoregisterSubjects#Mixed_head_models
https://neuroimage.usc.edu/brainstorm/Tutorials/DeepAtlas
If you need a clear access to subcortical ROIs and/or if you are not satisfied with unconstrained orientations on the cortical surface, I recommend using volume source models:
https://neuroimage.usc.edu/brainstorm/Tutorials/TutVolSource
https://neuroimage.usc.edu/brainstorm/Tutorials/CoregisterSubjects#Volume_source_models