Simply put, where are the bathrooms?
Historically, the easiest way to do this would be to dig a hole in the ground. This is obviously not an option in a habble. The second way to do this would be to have an actual sewer system. You'd have to overcome the following issues:
1) You really need a large supply of running water to flush things down. Sure "water gets collected", but unless there's only a few public toilets, that's a lot of water for use.
2) Miles and miles of pipes. These would have to be crisscrossing the bottom of each habble (presumably with some sort of incline so all the waste gets to the right place).
2a) Plumbing would be a nightmare. Consider that someone eventually is going to try to flush the wrong thing down the toilet. In a regular setting, you can dig down and clear out the blockage (though manhole covers would allow access to the bigger sections). Problem is, you can't actually dig through the spirestone. Thus if something gets badly blocked in one of the smaller tunnels, you are royally screwed.
3) I can imagine putting up new walls/vatteries/etc. throughout the spire, but think about hooking up a new house/vat to the existing sewer system. You either have to use an existing hookup, or add pipes, etc. above ground.
4) Doubly so for habble Landing. They need to have a source for water for everyone (kinda hard if it's a fountain in the floor), and need to have good sewer, otherwise it would be very unpleasant for the people living below.
5) Think also where all this sewage goes. On Earth, this this goes into the ground, eventually decomposing, etc. Here I'd think you'd essentially need to take it outside the spire.