This is very very odd .... a quiet word surely would have been enough
There must be something else - and that has to be something very different.
As he's still in the RN (for now) it has to something related to the ship I suspect rather than some generic "failing" (wine , women, song would be out of the service)
He probably expressed some strong thoughts on a pet subject of someone closer to the top (I doubt it would be the SecDef who got involved here) - and that is why he was stitched up