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It is common for a cruise line to hold passports during a cruise, as many of the immigration officials may want to inspect them while clearing the ship in lieu of having the passengers individually present themselves with their passports. It is never a problem, however. When you check in they will give you a receipt for the passport and then sometime after the final port of call and arrival at your destination, they will make them available for pick up at the purser's desk (or some other appointed location)
It would be unusual for a ship to hold them on a typical Western Caribbean itinerary, though.