Imagine that I have a device that gets inserted into a car engine to speed up the car. It consists of 3 parts that are connected via tubes. Is it an apparatus that gets inserted into a system (the car engine) or is it a system that gets inserted into a car engine (system)?
There is no hard and fast distinction between a system and an apparatus and it doesn't matter much. The actual statutory categories do not include either term. In 35 USC section 101 the listed categories are process, machine, [article of] manufacture, composition of matter and improvements to any of those things. An article of manufacture is something made in a manufacturing process. And a machine (originally and loosely) was something with multiple, interconnected moving parts.