The computer knows there is a fan because it knows when there isn't a fan. By subtracting where there is a fan from where there isn't a fan, or where there isn't from where there is (whichever is greater) it obtains a difference, or deviation...
How does the computer knows that? You mean the parts that can meassure temperature will meassure where it gets warmer, or where it doesn't get warmer, altough it should?
How does the system knows, it is not a local heat pipe, transferring heat away?