There are 10s of thousands of small sub or near sub water obstructions thru the world--not all are charted. We have found several, just sailing along in remote areas. When we do, we go back over the area, verify the position and then report the obstruction (it might be 30 feet, no problem for us in small boats, but can raise Heck on an air craft carrier!
Sometimes an obstruction may be on one chart set and not another, such as NOAA or DMA vs Admiralty. There are many chart systems.
As I noted digitalization may cause errors. But, many--most of these are not well seen on satellite images. Reason is because they are jus sub surface or very small--and there is not much shipping --except Minesweepers and Submarines. There are lots of atolls with wrecks all over the world. Many of these are fishing boats which should have local knowledge.
In this case, there is a light house which is a fixed reference point, with known GPS co-ordinates. Why the watch keeper was not aware of this is beyond me. When piloting in remote waters, one needs all of the information available. All of these structures are recorded in sailing directions or other similar publication. We always carried Light Lists, sailing directions and charts aboard (sometimes up to 2,000 charts). Plenty of room for many charts on a mine sweeper.
I don't see this as a Navy or Safety problem--it was just one or two individuals who were not prudent...and as Charlie says, they are gone!
Too many of these happen. Such as the cruise liner.