You mean that you see such “holes” in the mesh as in the picture? I confirm that they appear quite often.
Maybe it is a Gmesh/Netgen issue rather than a PrePoMax or Calculix issue, or is it?
Well, almost for sure if these flaws are generated by meshers (unless it’s just a visual issue). This usually comes from broken geometry (it may also have missing faces). Looks for orange warning signs.
But the issue mentioned by the OP is probably something different as the mesher reportedly fails to mesh entire geometrical surfaces. Of course, the geometry can be suspected here too and needs some checks as well as potential repairs and simplifications.