The interesting holes in the marble blocks are where peoples of past centuries have scavenged the metal that was once used to lock the marble blocks in place.
I would guess that the recovered metal was used to make weapons or armaments. Ephesus was probably just considered a heap of old rubble in those days and they did not realize that they were defacing something that later generations would hold as a classic gem of heritage.
Howard [ Just Imagine ] 28-Nov-2006