@User: Use "feedback find" to go to specific error areas, and "feedback why" to report on the reason. It will not tell you which layers are overlapping, but you can do an area selection on the area of the feedback, which is marked with cross-hatched lines, then use the "what" command to find out what is selected in that area, to figure out what the overlapping types are.

Those boxes are empty and therefore report no DRC. Is it possible due to some bug in Magic extraction because those areas are part of user_project_wrapper and not part of the hardened macro which means that they have no transistors beneath them.

It is not a DRC error, it is an extraction error. If the extraction is done from a script, then you won't find it in the layout. If so, and you want a dump of the feedback created during extraction, then follow the extraction with "feedback save <file>".