The victim is supposed to have been found in the Red Sea. However, the critters shown to have eaten the victim include a 'Blue crab' (Calinectes Sapidus) which is only indigenous to the eastern Atlantic coast - not the Red Sea.
The dead marine is found in a body bag. However we later find out that the Mossad agents sank the ship after killing everyone on board. There is no point in putting just one body in a body bag, especially since the given reason was that bodies are stored that way in the ship's freezer. No body was stored in the freezer. All the bodies were left where they died.
(at around 1 min) Ziva is handed a cup of tea by a Jordanian ship captain. She takes it with her left hand, which is an insult in Muslim countries, and Ziva as a Mossad agent should be aware of this. Yet the conversation goes on as if nothing has happened.
In Malachi Ben-Gidon's recount of events, shown in flashback form, Ziva states "Too far at sea for radio to land". Apparently Ziva does not know about HF radio which can provide global coverage. Of course, it is possible the Damocles doesn't have HF transmit capabilities, but Ziva probably hasn't had the run of the entire ship, given the lack of trust between crew and passengers, and would not know for certain. She may have noticed a lack of antenna, but it would be fairly unlikely that the ship doesn't even have an HF receiver (for weather warnings, etc.), which would require an antenna.