Because nothing is perfectly flat even in our world -- there's always a small incline. It might not be detectable without instruments, but it will be there. Consider also that even if the original builders settled the spires perfectly upright, building tend to sinks and the earth moves. Unless there's some self-correcting mechanism, there's no way it would remain perfectly level.
Note also that all building tend to sway (in wind, minor earthquakes, etc.). Yes, spirestone is incredibly strong and a spire is relatively short and squat, but it's physically impossible for anything to be 100% rigid. It doesn't matter how tough it was built, something 2 miles high is going to be moving, possibly vibrating back and forth as the waves move up and down the spire.