If you can send me the example file, I can possibly take a look.
I am currently working on making the structures stuff better, so having failure cases is timely.
Make sure you're running the latest version of OpenVSP. I've made some recent improvements to the surface intersection code that might help (but might not).
Any CAD tool should be able to trim the un-trimmed surfaces. You might need to turn the wing surface into a solid first. You'll need to seek help from someone who knows how to work whatever CAD tool you have access to.
Rob