Archaeologists are not always too careful either. We should keep in mind that the skull was apparently buried under something for a long, long time. Lucky it survived at all.
Once a site is designated for excavation, the tools used wouldn’t produce this kind of damage. I suppose if the skeleton was found from a test hole it could be damaged. There would be very low odds of finding anything in a test hole but I do recall someone pulling an adze out of a test hole.