If you don't want rock waste scattered around all of your extractors, place burial sites nearby so your drones collect waste in one convenient location.
As your extractors continue to extract useful resources from the planet, they continue to accumulate waste. However, there is a certain technology in Surviving Mars that gives your drones the ability to convert rock waste into concrete. It's called Liquefaction.
In each mission, the tech tree drops out randomly, so there is no information about when you can research waste liquefaction, but this technology is in the engineering department. The amount of research depends on how deep the technology is in the tree. If you're lucky, it'll only cost you a few thousand. If not, then ... it will cost a lot more.
After you complete your waste liquefaction research, your drones will take responsibility for blasting all those pesky rocks into usable concrete.
Make sure you have enough concrete storage facilities and you have a sufficient number of drones operating in the same area as stone waste.