It helps us to visualize relationships and helps us to communicate. We might use a very simple system based on size and say some things are big and other things are small. The point here is that with some classification systems the basis for the system is a relative continuum. In such cases there are no well defined boundaries or lines between what is big or what is small, so we decide that we will draw lines to separate different categories.
Problems arise when someone says the lines are in the wrong place.
Often, in scientific circles, papers are published arguing where the lines should be and eventually we reach a rational consensus, at least for communication purposes, as to where the lines should be. But, considerable debate often remains. For instance, in the classification of plants and animals, a robin is a robin and never a blue jay. Yet in other classification systems, we have situations where the things being classified don't always fit into the same category. So we place it in that category where it fits most of the time.