When Homer's mother uses the phrase "filthy pit," in many ways she is referring to everything that the coal mine has taken from her, her husband, their time together as well as with the family, and now she is referring specifically to the incident with the mine collapse.
In this case, some of the shale collapsed at the coal face and trapped some of the miners. Homer's father went down to help the rescue team despite her begging him not to.
Eventually he emerges with a horrible injury to his head that leads to him losing his right eye, and one of the miners is killed though all the others are saved. Unfortunately for Homer, the miner killed is Ike Bykovski. Of course he feels responsible for the death since it was his work with Ike that caused his father to send him into the mine.