Those look like missing faces. What are you're compile tools? I occasionally have that issue using the latest version of VHLT. SourceSkyBoxer talks about this problem being alleviated by UMVHLT but I have never tried this version of the tools myself so I can't verify if this really fixes this issue. That being said, I personally have only experienced that issue on angled brushwork.
If you are using VHLT, try changing those brushes to func_detail. It will usually fix the problem. Of course, this is only ideal if you do not need that computer to seal the map (easily fixable) or block vis.