I've come across some truly revolting geometry artifacts which happen when carving on surface constraint using a really tiny sphere brush.
Best way to explain it is compared to the effect you get on the outside of a mesh when adding tiny claysphere and you run over a corner at enough of a tangent and it shoots those little perfectly straight "wires" across the gap. I'm guessing anyone who's used tiny sphere clay add constrained to surface will have seen them, right?
Well this most grotesque of glitches seems to be related to that but instead of "wires" it's firing miniscule tubes right through the mesh but, if they're small enough, they don't form complete tubes but kind of break off into little fragments of pointless polygons, inside the mesh itself.
Worse still, if you're unlucky, the point on the surface where the tube originated can get seven shades of messed up on export as geometry gets sucked inside the mesh, polys flipped and intersected and all manner of gross and yucky.
Here's a pic where I'm looking through the surface of a cube-shaped mesh, with the tubes marked. It's kinda confusing pic cos I'm sticking my head half inside the mesh but those bits I've highlighted are not visible. Only way to fix it is to add clay over them but this is fiddly cos they can go right up to the surface and working inside the mesh is disgusting at the best of times.
Here's a drive link to the sculpt. https://drive.google.com/file/d/0B-a8Bp8gNkI6dlpmajI0U240UDA/view?usp=sharing