The terrain clips through the copper deposit, and the copper deposit is made up of several 'nodes'. The whole deposit is solid, some think it's actually hollow, but because the nodes can be large and they break as a whole this leaves quite a bit of clipped through terrain before you find the next node.

Devs kinda have a problem here. Dirt can't be partly at one level and partly above, so the only way to not clip terrain through the deposit is to set terrain below deposit level - however then all deposits will be fully exposed, no blending into terrain.

Probably the best thing devs could do it have nodes terraform terrain that clips through them on destruction, partly exposing surrounding nodes.

This is just my laymens take, I have zero connection to the devs, nor have I even read most of what they've said about valheim.