Placing the parts into the machine, the parts don't leave Indy's hand; a duplicate just appears in the socket.
The CIA's field members are known as "officers," not "agents" - an agent is a foreign national who provides the CIA with inside information.
When Indy dives into the wreck of a battleship, he opens a hatch with a hammer. The water level inside the hatch is a couple of meters higher than the sea level. The water level should be the same since the hatch and the sea form a system of communicating vessels.
At Palawan Lagoon, Indy must uncover a hidden underwater door. Beyond the closed door is a shark and another closed door to get through. If the doors are the only way into the chamber, the shark couldn't get in. If there *is* another entrance, the gameplay with the doors is pointless.