Even a small planet is a big place, so it doesn't necessarily need to be hidden. It can be observed and even documented. It just needs to be dismissed. IMO this makes it so much more interesting. It just needs to be plausible. Because if we were ever to discover evidence of an alien presence on the moon (or discover Atlantis, for that matter), reality would seem totally implausible, compared to anything you might conceive.
An oversight in Lunar mapping, combined with the age of the facility.
A large (but indeterminate) number of years ago, an unknown agency which may have been of either terrestrial or extraterrestrial origin visited the moon and built a large base below-ground, but with a significant number of above-ground structures spread over approximately 20 sq. km. Over the years, these structures were damaged by micrometeorites and partially-covered by regolith, but they remained largely visible both from the surface and from orbit, once selenologists knew what to look for.
Early Lunar mapping efforts spotted these structures. However, they were looking for natural formations, not artificial structures. Because of the fact that the outlines were softened by damage and cover, there was nothing to indicate by computer analysis that they weren't natural, and human analysts determined that they were an unusually-regular rock formation. No further investigation was done, and further scrutiny wasn't given to them in later mapping efforts because they had already been identified.
Jump forward in time...a group of Lunar geologists decides to investigate these rock formations first-hand, to determine why they're so regular. When they arrive, it's immediately obvious that they're artificial, causing the leader of the expedition to exclaim:
Holy mackerel! How the heck can we have missed something this big on a planet this small for the past five hundred years?
...or something with a similar meaning, but not family-friendly.
Once observed, a review of old data showed that it should have been obvious that they were of an artificial nature.