Probably, highly probably, caused by vertices off the grid (which happens a lot when you're carving with any brushes more complex than a cube, or with rotated brushes). Those vertices are put on the nearest grid point during the compile process, which sometimes results in non-planar (not completely flat) faces. That's a source of trouble...
I'd advise using multiple brushes in such situations, rather than shaping one single brush as much as possible. Also, clipping instead of carving, and vertex manipulation (though you'd better learn how to work with it before you go crazy with it, it's easy to create trouble with it).