Based on the threejs demo on clipping + stencil (three.js examples), it seems that when dealing with geometries that are very “thin” (or very close to other geometries?), they appear to mess up with the stencil planes (see capture attached)
There we shouldn’t see the yellow or the red parts (and the blue caps are a bit messed up).
The merged geometry come from a GLTF model.
I’ve tried various things without much success.
Edit: I’ve added a fiddle to demonstrate the issue that I suppose is related : Edit fiddle - JSFiddle - Code Playground
The plan in the ‘back’ of the cube is causing issues when added to the merged geometries.