Hmmm...I test with your file on
- FreeCAD_0.19-21775-Linux-Conda_glibc2.12-x86_64.AppImage
- FreeCAD_0.19-21329-Linux-Conda_glibc2.12-x86_64.AppImage
and still can't get your result.
Can you post your ifcImport/ Export setting for reference.
BTW, I had no problem in export wall with subtraction in the Villa Savoye model... maybe need to test that model again ....
Thanks !