Building a structure over zoned buildings, as agent86's comment points out, counts as bulldozing the building and dezoning the land. Recall that in SimCity 4, bulldozing zoned building requires the city to buy then decommission the structure from private hands, which means that doing this with hi-rise apartments or office blocks can be quite expensive. You will also of course displace any citizens living or working in those zones as you demolish the buildings.
In addition, in rare cases when building a small structure such as the 1x1 bus stop it is possible to create zones which cannot access roads anymore. For example, take a 4x4 zoned area (
< indicate the direction of the zone):
If we build a bus stop at
s, it is possible that the zone marked
* could become trapped. This is rare as the game usually intelligently realigns the zones so that they always face roads, but it is possible to happen if this area was occupied by 2x1 buildings.