From the article it appears there was an older chart on board that showed a possible hazard in the area. I have no idea what scale the chart was, but my guess is it was a small area chart (local type) rather than a large area, usually used for transit. If it had been an older, outdated chart, it would have been deep-sixed and not on board.
So, as an ex-navigator, my guess is the small area chart was not checked and it was assumed the large area one was fine for the transit. That is a big no-no.
Also, from the other post on his punishment, he was assigned to a basket case to get it in order. Nav may have been low on the list.
I was sent to such a ship, but as an XO. The CO put me to work on the admin part of my duties but left the navigator part to an old timer. We went aground (an LST but we were not supposed to go aground where we did) and I was immediately assigned as the investigator and also, Navigator. I found we ran aground on a not-charted sand bar. (It was probably more the wash from our screws as we tried to get off.) The CO (a Lt), took full responsibility. Nothing happened to him. He had a great career (including Presidential aid) and was a Captain on his way to Flag when he unexpectedly died of a heart attack.
I think I might have heard on the radio that Mooney disregarded the second chart.