Earthquakes were indeed a problem for Mesoamerican engineers. The Aztecs even believed that the 5th sun would be destroyed by an earthquake. Considering how vulnerable the Valley of Mexico is to shockwaves their concerns were justified. And we can see there responses in their architectural style. Larger buildings, such as pyramids, often used architectural features intended to limit earthquake damage. For example, Teotihuacano architecture utilised the talud-tablero style which helped dampen the effect of tremors, and many cultures built their palaces on platforms that ensured strong foundations. Furthermore, Mesoamericans tended not to build up too much, so their buildings were not as top-heavy. Common houses, being built of much lighter material, were likely resistant to earthquakes as well. However, they were ultimately simple constructions, and were easy to repair.

All this seems to have worked. The 2017 earthquakes in Mexico seriously damaged a large number of buildings. But most archaeological sites suffered either minor damage, or no damage at all.