When using any cutting or slicing tool, make sure that you are fully aware of what you are cutting. Most applications have the ability to define what is being cut. The most common example is if a cube is being sliced, that the cut affects (or not at the artist’s discretion) the polygons at the back of the cube to make a volumetric cut.
Most applications have the ability to only allow cuts to be applied to selected elements. This can be really handy when a mesh object has several parts of disconnected geometry within it and only one needs to be cut.