When they find intact buildings like that they were usually buried by some natural disaster like Pompeii or intentionally buried like Gobekli Tepe.
Usually when they say they’re finding older cities under the newer ones they just mean the traces of the city, usually the foundations like in the case of Troy. In that case the city has usually been destroyed by fire and the people there built atop the ruins.
Sometimes it’s just a building that got sealed up for one reason or another and built around so much it was forgotten about. Remember building codes are a new phenomenon.
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