It concerns graphics, Z-Ordering specifically.
Tailings pond is masking some parts of vanilla objects too. eg. wooden power poles, but not the cable hangers at the top.
Also, while it doesn't just affect pYCoal, but other parts of the pY suite, I'll post this feedback/request here:
Tall buildings hide what is immediately behind them, and I have often failed to make a fluid or belt connection as a result - pipes and belts do not highlight the connection in the same manner as inserters - They also hide supply lines running parallel to these buildings. The Tholin collector does have a nice feature where the balloon fades in and out with the zoom level. Extending this feature to the taller buildings allowing us to see behind at high zoom levels, would make life a great deal easier.