Excavation pits can be clean and I'm pretty sure they would have considered what was left in the pit.
What you're thinking of is the processing aspect of mining, which is a whole different beast.
This really depends on the composition of the minerals. Butte, MT is famous for its pit that is filled with highly toxic water: https://en.wikipedia.org/wiki/Butte,_Montana#Berkeley_Pit (or https://www.youtube.com/watch?v=n-Ej2EtE744 ).
No, not exactly. Many kinds of rocks and soil will release Acid Mine Drainage (AMD) or otherwise release sulfates and heavy metals into the environment. Of course a lot of this will already be known from the treatments they had to do when keeping the water table low when mining.
When I was a kid I remember a number of very old stone quarries that had been allowed to fill, then years later they had to put up warnings for people to stay out because the high Ph water was dissolving metals into it.