Summary:
Those who believe that there are intelligent extraterrestrial beings who are visiting our planet, must also assume that Earth would not be the only place in the deep emptiness of space that they would travel to. Even using advanced propulsion systems, the great distances between solar systems, planets, and moons would almost certainly necessitate a stopping-off place, or rest area, if you will. This would, of course, allow for maintenance, refueling, and a break for the occupants of the long journey, or possibly a change of crew members.
Small Cities:
If these assumptions are true, then there is a good possibility that these way stations or rest areas would spawn a creation of structures to store needed supplies like fuel, food, and parts, and also housing for communications equipment. This in turn would require personnel to run the stations, and live there, which would also require housing and the necessary requirements of life. These small cities, even if partly or totally underground, would have a certain amount of visibility from above.
Signs of Existence:
Even the most discreet space station would have some sign of its existence, like a beacon for incoming ships. If alien races were visiting Earth, and wanted to remain secretive, it is very possible that they would choose the far side of the Moon for a station location, it being a short distance from planet Earth, and yet hidden from telescopic and photographic view. The only time that these structures would be visible is when earthlings visited the far side.