[Varda]

I guess the original find could have been by someone accidentally hitting the skeleton with a shovel. Once the site was handed over to the archaeologists this kind of damage wouldn't happen.

I know that it's common for archaic era skeletons to show signs of a violent life and death. That made me think of the hole as the cause of death.

[SunkenCiv]

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.