First of all, it's important to understand nodes. Every physical object you create is composed of 2 nodes, the Shape Node and the Transform Node. The Shape node handles all the physical properties of the object, such as manipulating vertices, creating deformations, etc. The Transform node handles all the location aspects of the object, such as where it is in 3D space, rotation, scale, etc.
So, sometimes, when you affect objects with different actions, it creates new objects (such as when you combine objects together or convert to other geometry types) and some nodes get left behind.
To clean these quickly, go to File > Optimize Scene Size. This removes these unnecessary nodes. Note that this also gets rid of unused materials and textures and other things like that.