People also didn’t have the software and hardware tools we have now. As a result, many old churches in Europe were the result of trial and error. Even though you got the most experienced architects and engineers, building large stone buildings is still hard and mistakes happen. As a result, cracks begin to form, and walls were reinforced later to prevent the whole thing from collapsing.

Nowadays, you would just simulate the whole thing under various situations and fine tune the plan before even ordering the construction materials. If that’s not an option, you just have to accept the fact that you’ll discover unexpected things at inconvenient times, and you’ll have to adapt.