Harry's drink (which is laced with booze) changes level between the bar and the table.
Much is made of the importance of the buoyancy balloons when crossing the seaweed. Yet they are not large enough to do much good, they don't float upwards, or need to be tied down when not in use, and near the end of the film they are not needed anyway.
First Officer Hemmings says hurricanes can be precisely predicted and tracked. It isn't true now and certainly wasn't when the film was made/set.
The Spaniards all speak modern English. (They need no translators to speak to either the modern castaways or the descendants of the religious refugees.)
When Unity and Harry are in the bar after getting back in the ship, she
makes Harry a drink. When he sips it and realizes it contains
alcohol, the glass is nearly full. When he throws the glass
towards the bar in a rage, the glass is completely empty.
At the beginning of the film the captain performs the eulogy for
El Supremo and they then bury him at sea. On top of the wrapped body lies a sword.
As they tilt the body the sword falls towards the water. As the body hits the water
there is no sign of the sword at all or the splash ripples it would have caused.
The containers of Phosphor B appear empty (considering how easy they are to lift and how they wobble when jostled)