Hi Corinne,
Two of the BEM surfaces you generated are intersecting.
Start by making sure the all the surfaces look good, by displaying the inner skull, outer skull, head and cortex surfaces in the same figure. From the surface tab, you can change the color of the different layers to help with the visibility. Set the smoothing to 0% for all of them. Please post the results if you're not sure this is what it should look like.
If your surfaces look good, you could try to get rid of this problem by computing BEM layers with different numbers of vertices (prefer keeping the same number for the inner and outer skull layers).