Originally posted by ogre513 (CryMod)
One easy way to fix this is to select all of the objects in your scene and then go to point select mode, after this use the filter points tool. This tool can be found under Model > Modify > Poly.Mesh > Filter Points.

Check your polygon count before and after using this tool. After using it you should notice your polygon count drop a small amount.

This tool will get rid of any doubled polygons or other errors.

I have found that using the boolean tool often cause degenerative errors on occasion.