what version of three are you using? I can no longer replicate the problem with the latest versions…
three@0.173.0
three-mesh-bvh@0.9.0
three-bvh-csg@0.0.16
the problem I had before was using double sided materials (workaround was setting material.side = 0 before operations) with the outdated versions:
three@0.148.0
three-mesh-bvh@0.5.24
three-bvh-csg@v0.0.2
I’d suggest setting up a live example with your setup, here’s a starting point…