The term ghost in the machine was first coined by a philosopher called Arthur Koestler.
Is this term common enough that almost every native English speaker has heard of it?
As suggested, Google Books can give some indication of how frequently an expression is used in writing. The expression comes from philosophy and its usage appears to have increased in recent decades. There is no evidence that it has become a popular expression, though its usage by computer programmers may have helped in that respect as suggested by the Grammarist.
Ghost in the machine is a phrase that arose in the field of philosophy, though it is slowly making its way into more mainstream English usage.
The ghost in the machine means the consciousness or mind carried in a physical entity. Gilbert Ryle coined the term in his 1949 work The Concept of Mind as a criticism of René Descartes. Descartes believed in dualism, the idea that the human mind is not physical, that it exists independently of the human brain. Ryle referred to this idea as the ghost in the machine. He believed that human consciousness and mind are very dependent on the human brain. The term ghost in the machine has come to also describe the supposed consciousness in a device that behaves as if it has a will that is independent of what the human operator wants the device to do. Computer programmers have appropriated the term ghost in the machine to explain when a program runs contrary to their expectations. The idiom ghost in the machine is a metaphor, which is a comparison that is made figuratively.