Many new users of WWMT find themselves confused when it comes to the setup of WWMT. This is primarily because there are some specific paths you must set correctly for the automation of WWMT to work.
This error usually indicates Steam did an update or you are working with a mod that doesn't use the Steam VProject setting. Read the fix here.
Fixed in VMF Exporter 1.21 (WWMT 1.768)
The current VMF Exporter does not yet export the correct texture alignment, rotation and scaling on brush geometry and displacements.