During discussions about damage to the American destroyer, it is mentioned several times that both the Captain's stateroom and the Combat Information Center (CIC) were struck below the waterline and flooded. However, both of these areas are located on the "O-1/O-2" levels of an Arleigh Burke class destroyer. well above the water line, and external shots of the destroyer show this area of the ship as undamaged.
When Agent Wells speaks to the hostage-takers via a cell phone Secret Service Agent Ritter delivers, there is a dial tone after the line is disconnected on the other end. Cell phones don't have dial tones after a call is disconnected.