If the aircraft ran out of fuel waiting for the deck to clear, that's not one of your 'part and parcel', things go wrong at sea' occurrences. Nor is it 'part and parcel of active ops'.
If true, it would indicate a basic lack of ability to properly plan and execute a fly pro from the deck.
I'd also be interested to know what 'waiting for the deck to clear' meant. Aircraft parked in the landing area? Damaged arresting gear? Previous aircraft stuck in the landing area? Looking at the report, it appears that the first of three aircraft landed, the second ditched, and the third diverted.
However, best regards as ever to all those of whatever nation doing their bit at sea,
Engines