When instanced meshes were using FBX geometric transforms, the code was not telling ufbx to create proper adjustment helper nodes due to UFBX_GEOMETRY_TRANSFORM_HANDLING_MODIFY_GEOMETRY_NO_FALLBACK flag. That flag was put in earlier, before import of armatures was solidified, turns out using the proper flag (UFBX_GEOMETRY_TRANSFORM_HANDLING_MODIFY_GEOMETRY) is not a problem anymore. Pull Request: https://projects.blender.org/blender/blender/pulls/145527