Thanks for your reply @mmittal.
We have noticed these warnings only occur for a specific asset and when we access the sub-elements of the asset using the API (e.g., using XformPrim.get_forld_pose to access the bolt_M5X16_tight element of kona_module). This asset is directly imported from Onshape using your Onshape importer. Moreover, the aforementioned undesired effects seem to be related to another problem.
What do you mean by repro, a USD file? If so, how can we share one with you?