The VMF Exporter 1.17 and older had a bug that would cause scenes with non geometry in layers labeled Convexity Floors and Convexity Walls to get duplicated each time the scene was exported to VMF. That bug was fixed in WWMT 1.766. After that update, the VMF Export dialog should read Version 1.18 or later.
It is important to get that fix to avoid any possible explosion of file size. (In one set of tests, I had successfully made 32,000 extra nodes in the scene before I noticed the dilemma because the exporter started to slow dramatically and Max itself was starting to crawl).