If you're using OpenStudio, in SketchUp, tun the OSM Diagnostic Script: Extensions -> OpenStudio User Scripts -> Reports -> OSM Diagnostic Script

That includes the option to delete problematic surfaces, but you probably want to try finding and fixing them first as the auto-remove may mess up surface matching.

If in raw EnergyPlus, enable Output:Diagnostics,DisplayExtraWarnings for more detail on the degenerate surfaces.