I have noted that ships that I see during the 'enemy movement' replay step disappears from the map when it is my turn to move. The hex the ship is in is shown as it is not covered by the fog of war so the ship should be visible. Note that the ship is still marked with a dot on the strategic jump map. I cut together two pictures showing this below. In the one to the right I am considering bombing the 'invisible' ship with my bomber.