Well same reason why we have abandoned industrial complexes, old abandoned buildings and such. People need to be willing to do something with that ground. Removing ruins takes time and money too... the amount of just burned down or abandoned buildings that litter our modern landscape is quite vast too.

In many cases ruins also just just stay landmarks

This is today. Back then all they had were hand tools...not explosives, heavy machinery, cranes and all that.

You are not just "removing" structures that are as solid as lets say the roman colluseum

Often times ruins also tend to be mostly foundations.. no one bothered to remove foundations

So they very much did remove a bunch of it. Just.. put dirt over it and use the square as a market or something.

Other times.. well cities get abandoned by conquest too... whoever conquered the place doesnt necissarily see maintainance of some places as needed.

If europe wasn't rebuilt with massive efforts after ww2 most of these ruins would still be here.. this is how many war torn countries will remain to look like for loong times.