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After the collapse of the Empire, Roman building where stripped and left to rot, floors where covered with dirt for making crops or just for hiding pagan images.

I am also amazed by amount of dirt, not by the fact it is covered (it came by process of top soil formation ); but by the sheer amount of it. If that was just after 2-3 thousand years, it makes me wonder what other things can we dig which are much deeper? But again not prehistoric kind of deep, more in range of last million years.

Umm fossils maybe?

There's no rubble over the floor so it's most likely silt or mud from flooding/mud slide.