New Stuff And Old Stuff

The wonderful Brain Cox was on TV and stated that nothing is new and even the atoms making up our bodies have been other things before over the course of life on Earth so our arm may contain part of a plant that the first fish trod on as it left the Ocean and our left ear could contain some of the water which our tree dwelling ancestor peed out over a squirrel which is now in our little toe.  
All very mind bending i know to consider that we could be breathing in oxygen and drinking water that dinosaurs and ancient plants used millions of years ago but such is the circle of life that we eat plants and animals and their atoms become our bones, blood, and skin and when these atoms which make us will go back into the soil and air when we die to become new plants, animals or even part of a motorway pillar at some point in the far future.
He also said that at some point around 900,000 years ago 98.7% of the human population got wiped out due to extreme climate changes, severe droughts and dropping temperatures in Africa which caused extensive loss of vegetation and a sharp decline in the grazing animals that early humans relied on for survival, leaving just around 1,280 breeding individuals to keep us going and it took millennia before we got going again so while some species bounce back, others don’t, but we’re probably the first ones endangered because we did and then stupidly stuffed up the air, water and ground we need to live.  
All this got me thinking, if nothing is actually new and things are made from previous things why do we have a problem with waste because everything that goes to make more stuff is made from the other stuff we dug out from the ground such as coal which is a fossil fuel which means setting fire to dinosaurs.
With recycling we convert the raw materials of old into new stuff but there is still a good proportion of new things that we have to dispose of but if nothing is extra to what we started with, so why is the new stuff not being used to fill the holes we made digging out the stuff to make it.
We must have massive holes all over the place we can fill and the new stuff isn't going to weigh more or occupy more space than what we started with because it is the same stuff but then maybe my Cerebral Cortex is part made from atoms which were once a Conker Tree because i'm obviously missing something here.