Lightning clouds are a type of sighting that implies but does not show the ship. This is equivalent to jet trails across the sky or the wake left behind a boat. A stationary cloud bristling with lightning is making the statement - a ship was here.
The lightning is caused by sudden air displacements when a ship leaves 3rd Density. The air surrounding on all sides rushes in, and depending on air currents in place at the time will either cause knocking as the air masses clap together or cloud formation and lightning if the air masses are sliding past each other. Where lightning clouds form the ships were usually large, and were moving at the point of exit, rather than stationary. Humans who could not see the ship due to a close blend with the surrounding backdrop are surprised to see a stationary cloud bristling with lightning topside, as no known weather conditions on Earth produce this phenomena. They correctly assume that something supernatural has occurred, and since the movie Close Encounters of the Third Kind dramatized this phenomena to indicate an approaching ship, usually suspect that a sighting has occurred.