The how is easy, the aircraft was flying below MSA for the area.
The why, is because the crew hadn't got a clue they were below MSA due to inadequacies in the charts they were using.
They knew perfectly well where they were, the chart displayed just didn't show them to be in any danger. That led to confusion when an obstruction was identified ahead, because the chart would be expected to show anything large or tall enough to cause danger to the aircraft.
It really doesn't have to be any more complicated than that.