The truth is that in some cases they didn't. Winchester Cathedral is a prominent example: built on the plain between two rivers, the cathedral was prone to such subsidence during its construction that basically none of its internal lines are parallel or perpendicular. In the early 20th century, the whole structure came so close to collapse that a frogman was employed to go into the flooded mud underneath the building and retroactively build a series of cement foundations to keep the building standing. You can read about his frankly heroic actions here. A common running joke among medieval archaeologists is that if you visit any medieval cathedral, it's a safe bet to ask when, not if, the tower collapsed.