Depends on what you agreed upon. The excavator should have taken away most of the soil/dirt and left some for the other contractors. Any left after that has to be hauled away and that usually costs money. "Cleanup" prior to surfacing the pool usually means clean out the pool. The decking subcontractor will likely remove any soil they disturb in their own grading but they won't take away someone else's debris.
You should probably have an honest conversation with the PB regarding this. The boulders/rocks will be costly to haul away and remove. Can you use them at all in you landscaping plans?
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i do have a 'plan B,' I can have an acquaintance with a Bobcat move the dirt around in the yard and compact it for about $500. The rocks, maybe 12 or so can be used within the landscape around my yard, it's just a pain to move them. I'm going to wait until the decking is done and address with the pool builder, the expectation written is not to leave a "war zone." As I said, it's clearly stated landscaping and "Lite" grading is up to me.