The bomb on the ship is set for 6am. In the action leading up to its detonation it is pitch black, yet when it explodes a minute later it is broad daylight.
Having served on ships in Vietnam, and knowing of actual ship explosions during World War II and Vietnam, a bomb placed in the main magazine of a ship would have cause a catastrophic explosion engulfing the entire ship, not a series of explosions as depicted.
During the church wedding scene the choir sings a hymn in Maltese (the filming location was Malta and the extras were mostly Maltese), although the story takes place in Portuguese African territory.
The crocodile that approaches Flynn after he has been shot has four fingers and a thumb on each hand, revealing it to be a human in a suit.
The archetypal English gentleman Sebastian, played by Roger Moore, would know better than to hang the British flag upside down, but he does so when he and Flynn set up camp in Africa.