There are still plenty of mysteries around known ancient civilisations, like for instance the
Minoans. One theory is that the legend of Atlantis was based on the catastrophic destruction of the Minoan's assumed military power base of
Thera by volcanic activity. An amazing civilisation which seeded the Greek world, left tantalizing artifacts and then just vanished - even from all historical record.
Little is known about the Indus Valley civilisations, though much work is now being done.
Also for large glacial activity affecting land mass, see how the island of Britain became cut off from Europe and
Doggerland was submerged by a combination of rising sea levels and a catastrophic tsunami caused by a massive underwater
landslide.
Like others have said though, if significantly advanced civilisations existed before this time you'd expect something to have turned up. If an alien 'earth base' was established on the cooling crust of the early planet, we're unlikely to ever know about it.