Mostly what they are talking about here is just dirt, in the same way the Amazon is just a river.
The process in question is called "mountaintop removal mining" and it is exactly what the name suggest. The mining company removes the entire top of the mountain to give them easy access to the coal inside.
That much dirt is a hazard, you can't just dump it in the nearest stream and expect it not to have some effects.
The government failed to due their part in controlling the permits, and then tried to retroactivly rewrite the rules to let all the previously illegal dumping through. Until the rules are cleared up the government should be blocked from issuing any new ones.
Jay