Many things can cause the build up of soil/anything covering a building - sometimes it's not a build up - and in ancient cities, many suburbs get abandoned for hundreds of years, so who'd notice?

It's a great question.

You get instances like Dublin where the Viking Thing Mound was leveled to raise the level of one street by some 16 foot or so. A great loss to the City!

I think it's in York where you can go below ground and see the first floor level of houses.

In a lot of cases it's just easier to rob away most of a building and cover it over in order to start afresh, so town planners just raise the level of the land to create a clean sheet.

Obviously, this isn't the case everywhere. Winchester is a great example. Apparently, the Romanised villas were abandoned there and people returned to round houses built amongst them. It must have looked odd with loads of stone-built ruins in an orderly-street-plan fashion with the huts set amongst them. Eventually, people moved on and settled in new areas leaving the ground to swallow up the remains.